Difference between revisions of "Opening Files"

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=== Program ===
 
=== Program ===
  
TDM Excel Add-In COM-API
+
TDM Excel Add-In (http://www.ni.com/example/27944/en/)
MATLAB
+
MATLAB (http://www.ni.com/example/30957/en/)
 
Python
 
Python
  

Revision as of 19:45, 17 October 2019

Add any unusual file formats here along with the programs that can be used to open, view, or edit the files. Many of these file types are viewable as plain text using Text Edit or Notepad. Several of these softwares can be accessed through UNC's Virtual Lab

This list is alphabetical by file extension.

To change a PC's default settings for opening a file type: In Control Panel, open up Default Programs. Go to Associate file type or protocol with specific program. Choose from the list provided, and click change program.

To change a Mac's default settings for opening a file type: Right click on the file, click "Get Info". Under "Open With" select the software you would like to use and click "Change All"


Contents

A

.ab1

Chromatogram files. Results of DNA sequencing are provided in three data files – .ab1 file, .seq file and .phd.1 file.

  • .ab1 files contain the DNA sequence electropherogram as well as raw data and some other information.
  • .seq file is a simple sequence text file in FASTA format.
  • .phd.1 file (Phred file) is a simple text file containing bases with quality values for each base.

Both .seq and .phd.1 you can easily open and examine in any text editor of your choice.

An .ab1 file can be opened with:

  • FinchTV (highly recommended; one of the most popular free software tools available for Mac that is easy to use) is a simple drag and drop for viewing and editing .ab1 files one-by-one.
  • GeneStudio (Windows only.) To open files, open genestudio, click Import, find file and open.
  • An R library, SangerseqR, is also available to load chromatogram files http://bioconductor.org/packages/release/bioc/html/sangerseqR.html

(For more info on how to work with .ab1 files, see https://www.seqme.eu/en/magazine/sanger-data-analysis)

.abf

Loads ABF2 electrophysiology recording files. Can be opened with http://cran.r-project.org/web/packages/abf2/abf2.pdf)

.accdb / .mdb

A file with either of these extensions is an access database and can be accessed using Microsoft Access. The database can also be accessed using the MDB / ACCDB Viewer, which is available for a MAC (a free trial version that is fully functional except for export limitations) and as a Chrome web browser extension. The MDB / ACCDB Viewer for the MAC can be downloaded from http://eggerapps.at/mdbviewer/. The MDB / ACCDB Viewer Chrome extension is available from the Chrome Web Store at https://chrome.google.com/webstore/detail/mdb-accdb-viewer-and-read/mcfgopgpdlpcphkcijidlencdankpgbc?hl=en-US.

.adf

Rasterized grid files. Can be opened with QGIS http://www.qgis.org/en/site/. More information here ESRI ArcInfo Grid (binary)

.adicht

ADInstrument LabChart files. Free viewer at http://www.adinstruments.com/products/labchart-reader

.ale

Avid (ASCII)

.am

Amira files. Proprietary. 

.amb

BWA (Burrows-Wheeler Aligner - tool for sequence alignment) index file. Along with .ann, .bwt, .pac, .sa files. NOTE: older version of software may generate more index files (.fai, .rpac, .amb, .ann, .pac, .bwt, .rbwt, .rsa, .sa)

.asc

Eye tracking data saved in ASCII/text format (ASCII); can be opened with any text editor.

B

.bam

Binary compressed version of a SAM file; viewable with SAMTools, a specialty gene-sequence viewer. View using the BAMseek program (http://code.google.com/p/bamseek/). Download the .jar file (http://code.google.com/p/bamseek/downloads/detail?name=BAMseek2011July24.jar&can=2&q=). Open the program, then go to File-->Open File. Browse to your BAM file to view it.

.bds

This may be a file with basedata from Biodiverse Analysis Software, which can be downloaded from GitHub (https://github.com/shawnlaffan/biodiverse/wiki/Downloads#available-downloads). Download the .dmg file and click to install by dragging the icon into your Applications folder. Once the software finishes installing, click on the icon to open it. Next, set your working directory to point to the folder containing the .bds files from the top navigation bar by clicking on File -> Set Working Directory. Then, also from the top navigation bar, click on Basedata -> Open. Navigate to find the .bds file, click on it to highlight it and press OK. The basedata should open in the application. If the basedata has arrows on the left, you can click on them to expand.

.bed

Genome sequencing format as output by a particular kind of sequencing chip. View using IGV, the Integrated Genomics Viewer. Open source application available at https://www.broadinstitute.org/software/igv/?q=download. Also possibly a binary sequencing output from Plink, if it's present in conjunction with a .bim and .fam file. Plink is open source and available for download at https://www.cog-genomics.org/plink2/. Binary sequencing output from Plink can be viewed on a mac as follows once Plink is downloaded and ready to use:

1. Download PLINK from https://www.cog-genomics.org/plink2/. The download consists of a folder named plink_mac that contains a few files, including an executable file called plink.

2. Copy the .bed, .bim and .fam files into the plink_mac directory

3. From the plink_mac folder in an open terminal window, type the following where filename is the .bed filename (without the .bed file extension) and outpedfile is the name you choose for a new .ped file:
               ./plink --bfile filename --recode --tab --out outpedfile

    For example, for the files exmpl.bed, exmpl.bim and exmpl.fam, the command would be:

               ./plink --bfile exmpl --recode --tab --out outpedfile

4. The outpedfile is a plain text file and can be viewed like any other text file (TextEdit, nano, using the cat command if the file is very large, etc.).

.bil / .hdr

Band interleaved by line (BIL) files are used for multiband images. They typically reside in a directory along with a .hdr file that has a matching file name. (For example, if you have a BIL file named image.bil, you should see a file named image.hdr in the same directory.)

QGIS can be used to view a BIL file as follows:

1. From within QGIS, go to the top navigation bar and select Layer > Add Raster Layer.

2. On the resulting popup window, use the "Files of type" pull-down to select the type "ESRI .hdr Labelled (*.bil *.BIL)."

3. Navigate to the location of the BIL file, then select the file and press the Open button.

For more details about BIL files, see https://www.qgistutorials.com/en/docs/open_bil_bip_bsq_files.html.

.bin

The .bin extension usually indicates that a file is in a binary format. There are a number of possible options for opening a binary file, depending on the exact format.

Some sound files have a .bin extension. You may be able to open the .bin file using the Audacity software package. You may have to import the file into Audacity as a raw file by choosing the following from Audacity's top navigation bar: Import > Raw Data. When a window appears, select the file to import. Accept the default values (unless you know how to adjust the values) and press the Import button. If the file is imported correctly, you should see a visual of the sound track in the main Audacity window. To hear the track, press the green triangular play button at the top of the window.

.biom

Biological Observation Matrix format

Use QIIME to access a .biom file in a virtual environment on a MAC by following the steps below. (See http://qiime.org/install/install.html for more information on installing and running QIIME.)

1. Open a terminal window.

2. Change to the directory with the .biom file.

3. If you have run QIIME before, go to Step 4. If you have not run QIIME before, create the environment and install QIIME by typing the following at the command prompt:

conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda

4. Type the following to activate and test qiime:

source activate qiime1

print_qiime_config.py -t

5. Type the following to get a summary of the table in the .biom file:

biom summarize-table -i some_file.biom -o summary_some_file.txt

6. For example, if the .biom file is named otu_bacteriaonly.biom, you would type the following:

biom summarize-table -i otu_bacteriaonly.biom -o summary_otu_bacteriaonly.txt

7. When you are done, exit the virtual environment, by typing the following:

source deactivate

C

.cdf

Common Data Format. One possible way to open the files is using Panoply viewer.

.c6

.c6 files are flow cytometry data files created using BD Accuri C6 Software from the BD Accuri C6 flow cytometer system.

.CEL

.CEL files are affymetrix gene expression microarray files that can be accessed using R.

Here are a few good websites with info on .CEL files: 

To open/view the .CEL files, do the following from within R:

1. Set your working directory to the directory containing the .CEL files by typing the following in the R console:

setwd("your full directory here with quotation marks")

2. Install the bioconductor package ‘BiocLite’ by typing the following in the R console:

source("http://bioconductor.org/biocLite.R")

biocLite()

3. Install the bioconductor package 'affy' and load the library by typing the following in the R console:

source("http://bioconductor.org/biocLite.R")

biocLite("affy")

library(affy)

4. Install the bioconductor package 'oligo' and load the library by typing the following in the R console:

source("http://bioconductor.org/biocLite.R")

biocLite(“oligo”)

library(oligo)

5. Read in the data by typing the following in the R console:

celFiles <- list.celfiles()

affyRaw <- read.celfiles(celFiles)

.cff

Connectome File Format

Program

"The Connectome File Format provides means to store arbitrary metadata as tags and in structured form for any so-called connectome object. Connectome objects encapsulate the various data types as they occur in connectome research." "The Connectome File Format Library (cfflib) is a pure Python library for multi-modal connectome data and metadata management and integration, based on the specification of the Connectome File Format (CFF). The cfflib provides a high-level interface to many common data formats by using Nibabel for basic neuroimaging data format IO, and NumPy and the Python standard-library for other formats." [1]

The Connectome Viewer is used ot view the .cff file. To run the Connectome Viewer in Mac OS or Windows, a virtual box is needed. See http://neuro.debian.net/vm.html#chap-vm for instructions regarding how to install a virtual box. Remember to set up a shared file folder to enable opening files located on your local machine.

Information regarding how to download, install and use the Connectome Viewer can be found at http://cmtk.org/viewer/documentation/users/installation.html.

Once the virtual box and Connectome Viewer are installed, from within the virtual box, open the terminal emulator by clicking on the terminal icon. Start the viewer by typing the following in the terminal emulator:

     connectomeviewer -v

Select File from the top navigation bar, choose to "Open the Connectome File," and select the .cff file.

Status

Nonproprietary

Ideal Format

.cff

.cif

Crystallographic Information Framework/Crystallographic Information File (CIF)

Program

CIF can refer to both the Crystallographic Information Framework, which is the "standard for information interchange in crystallography" and a Crystallographic Information File, which follows the standards set forth by the framework. (http://www.iucr.org/resources/cif)

There are a number of software tools for viewing and manipulating files in the CIF format (http://www.iucr.org/resources/cif/software#1). CrystalMaker is one of those tools that is easy to install and use.

CrystalMaker, which is used for interactive modeling and animation of crystal/molecular structures, can be downloaded (http://crystalmaker.com/crystalmaker/download/index.html) and used in demo mode without charge. On the CrystalMaker download page, select the platform you need (Mac or Windows) and follow the directions to download and install the demo version of the software. (Installation is straightforward.) Once CrystalMaker is installed and launched, you can choose among three options for opening a CIF file: (1) drag and drop the CIF file onto the CrystalMaker workspace (2) click on the filename to "Open with" (3) use the navigation bar to File -> Open.

Status

Proprietary

Ideal Format

.cif

.cram

Compressed alignment files (compression driven by the reference the sequence data is aligned to). The CRAM format is specified at ENA . Files can be manipulated from the command line using CRAMTools software or Samtools . They can also be accessed from a GUI using Integrative Genomics Viewer (IGV version 2.4 or later) .

CRAM In Samtools (instructions for Mac):

  1. In terminal, change directory to where your files are located 
  2. Add the Samtools executables to your path
    export PATH=/path/to/samtools-1.3.1:$PATH
  • To convert CRAM files to BAM, download the reference file and execute the following command:
    samtools view -b -T path/to/reference/file.fa path/to/cram/file.cram > path/to/where/you/want/file.bam
  • To write BAM to a plain text file:
    samtools view path/to/bam/file.bam > path/to/where/you/want/file.txt

CRAM in CRAMTools (instructions for Mac, still in progress):

NOTE: For v 3.0 of CRAMTools. To execute the jar file on Mac OSX, must have Java development kit (JDK) version 1.7 or higher installed. To see which version you are running, at the command prompt in terminal, type:
/usr/libexec/java_home -V
Latest releases of Java SE Development Kit  are available from Oracle (I downloaded JDK version 1.8.0_91)

To execute the cramtools-3.0.jar file, enter the following command in terminal:
/usr/libexec/java_home -v 1.8.0_91 --exec java -jar /path/to/jar/file/cramtools-3.0.jar 

  • To make running commands easier, set an alias:
    alias cramtools='java -jar /path/to/jar/file/cramtools-3.0.jar’
    • At the prompt, if you enter the alias (cramtools) and press enter, the cramtools menu should pop up
  • The CRAMTools README indicates this:
    To convert a CRAM file to BAM:
    > java -jar cramtools-3.0.jar bam --input-cram-file <input cram file> --reference-fasta-file <reference fasta file> --output-bam-file <output bam file>

CRAM in Integrative Genomics Viewer - IGV 2.4:

IGV 2.4 introduced support for sequence alignment data in CRAM 3.0 format for both a Mac and a PC. IGV can be downloaded from http://software.broadinstitute.org/software/igv/download. Follow the instructions on that page to download and then install the software, which at this time read as follows.

  • For a Mac: Download and unzip the Mac App Archive,then double-click the IGV application to run it. The application can be moved to the Applications folder,or anywhere else."
  • For a PC: "Download and unzip the Archive, then double-click the igv.bat file to run IGV. See readme.txt to run IGV from the command line."

Once IGV is installed, you can access a CRAM file using the IGV GUI.

  1. Load a genome (human, dog, mouse, etc.)
    1. At the left top corner of the screen, use the pull-down to select the appropriate genome for the data
    2. For more information on loading a genome see http://software.broadinstitute.org/software/igv/LoadGenome.
  2. Open the CRAM file (http://software.broadinstitute.org/software/igv/LoadData)
    1. From the top navigation bar, select File ---> Load from file
    2. Navigate to the file you want to open
    3. Double click on the file
  3. View the data (http://software.broadinstitute.org/software/igv/DefaultDisplay)

.csv

Comma-separated values

Program

"Microsoft Excel will open .csv files, but depending on the system's regional settings, it may expect a semicolon as a separator instead of a comma, since in some languages the comma is used as the decimal separator. Also, many regional versions of Excel will not be able to deal with Unicode in CSV. One simple solution when encountering such difficulties is to change the filename extension from .csv to .txt; then opening the file from an already running Excel with the "Open" command." [1]. For large CSV files, consider using a software such as Tad https://www.tadviewer.com/

Status

Nonproprietary

Ideal Format

.csv

.ctf

Compact tree file. Can be opened in TNT Tree analysis using New Technology software from Goloboff, Farris, & Nixon (2003). PhyloWiki TntWiki page created by Nick Matzke is helpful

    1. Open tnt.command file from the finder window
    2. Read and agree to terms of service to launch the software for the first time
    3. help; will list available commands
    4. help commandName will give a brief description of the command
    5. cdir /file/path (to change directory to where your file is located)
    6. shortread fileName.ctf (to read in the .ctf file)
    7. tplot ; (to plot the trees)

.czi

Image format for microscopes by Zeiss. The simplest way to open CZI files is using ImageJ and it's plugin Bio-Formats package.

To open a CZI file with ImageJ:

1. Open ImageJ software

2. From the top navigation menu, select File -> Import -> Raw

3. Navigate to the CZI file and select to open

D

.dat

Matlab

.dcm

DICOM file. For Mac, may use OsiriX image processing software to view, available at http://www.osirix-viewer.com. Also, you may use MRIcro for the mac, which is free from itunes (https://itunes.apple.com/us/app/mricro/id942363246?mt=12).

.DLD

OROBOROS Instruments DatLab Data file (see http://www.oroboros.at/?DatLab). Proprietary. No known open source viewer. 

.doc

Text document

Program

Microsoft Word (1997-2003)

Status

Proprietary

Ideal Format

.txt, PDF/A

.docx

Text document

Program

Microsoft Word (2007-)

Status

Nonproprietary, patented

Ideal Format

.txt

.dta

A file with the extension .dta is a Stata file created with the Stata application. There are a few options available for accessing this type of file:

  • Open using the Stata application located in the UNC Virtual Lab
  • Convert using StatTransfer at https://www.stattransfer.com
  • Open using R or RStudio with package foreign or haven. Following are steps to access the file using R/RStudio.
    1. Open R or RStudio
    2. Change your working directory to the location of your .dta file.
      If you are using R:
      1. Click on "Misc" in the toolbar
      2. Select "Change working directory"
      3. Navigate to the directory with your file
      If you are using RStudio:
      1. Select "Session" from the top navigation bar
      2. From the resulting pull-down
      3. Select "Select Working Directory" and then "Choose Directory"
      4. Navigate to the location of the data file
      5. Press the "Open" button.
    3. Load the "foreign" library by typing the following at the command line in the R console:
      library(foreign)
    4. Load your .dta file and assign it to a variable. The following example uses "data" as the variable name, but that can be replaced by whatever variable name is preferred:
      data<-read.dta("Your_data_file.dta")
    5. Once you have read the data file, you can view the contents by typing each of the following commands at the command line in the R console, pressing enter after each one:
      ls()                 to view all objects (tables) in the R database
      str(data)            to view the labels (column headings) in an object (table) from the ls() command  (may not work in some databases)
      names(data)          to view the labels (column headings) in an object (table) from the ls() command  (may not work in some databases)
      levels(data$XXX)     to view the levels of factor XXX in data
      data$COLUMNNAME      to view all the data in one of the single columns shown above
      str(OBJECTNAME)      to view all strings of data present in a given object (table)

.dwg

3d image file

Can be viewed in free browser viewer at https://360.autodesk.com/viewer

E

.edf

European Data Format files. Files can be opened using the edfReader library for R at https://cran.r-project.org/web/packages/edfReader/index.html

.edf

Eyelink Data File. Binary file that contains raw data output from the Eyelink eyetracker. The EyeLink Data Viewer (SR Research) can be used to view the file. At this time, you can find a trial version available for download on the SR Research site [1]. Once the trial expires, files can only be viewed in limited mode.

.eps

(Encapsulated PostScript Image File) Preview

F

.f2d

Fit2D file? See Fit2d software package, developed by the European Synchrotron Radiation Facility.

.faa

FASTA. Files can be opened in any text editor.

.fas

FASTA. Files can be opened in any text editor.

.fasta

FASTA. Files can be opened in any text editor.

.fastq

FASTA. Files can be opened in any text editor. For very large files that do not open in notepad++, use glogg (http://glogg.bonnefon.org/download.html)

.fcs

Flow Cytometry standard data file. Purdue University Cytometry Laboratories maintains a catalog of flow cytometry software at http://www.cyto.purdue.edu/flowcyt/software/Catalog.htm

Cytospec Software from Purdue University Cytometry Laboratories at http://www.cyto.purdue.edu/Purdue_software

The fcs files can also be opened using R as follows:

  1. If you have not installed flow packages previously, you should install them (https://bioconductor.org/install/). This should only be done the first time you use the flow packages. Once you have installed the packages, you will skip to Step 2.</span>

    To install the packages for R version 3.5 or later, open R/RStudio and first install BiocManager by typing/copying the following into the R/RStudio console and pressing enter to run the code and install BiocManager:
    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")
    BiocManager::install()
    

    Once you have installed BocManager, install the flow packages by typing/copying the following into the R/RStudio console and pressing enter:

    BiocManager::install(c("flowCore", "flowUtils", "flowViz"))
    

    If you are using a version of R/RStudio older than 3.5, type/copy the following into the R/RStudio console to install the packages:

    source("[http://bioconductor.org/biocLite.R http://bioconductor.org/biocLite.R]")
    biocLite("flowCore")
    biocLite("flowUtils")
    biocLite("flowViz")
  2. Type/copy the following into the R console to load the libraries: 
    library("flowCore")
    library("flowUtils")
    library("flowViz")
  3. Once the flow packages are installed and the libraries are loaded, change to the directory containing the fcs files you want to open by typing the following at the R console prompt with directory replaced by the full directory containing your fcs file(s).  Be sure to surround your directory with quotation marks. (On a mac you can drag/drop the file onto the R console prompt from a Finder window and the full path will appear.) 
    setwd("directory")
  4. To view an fcs file, type the following in the R console with filename replaced by the name of the fcs file you want to view:
    fcs = read.FCS("filename.fcs")
    print(summary(fcs))

    .fdi

    Network Draw files; open with either Network or Network Publisher (free) software [2]

    .fid

    Bruker 1D NMR raw data file. Bruker Topspin processing software is free to use with academic license. iNMR is another software available for Mac and PC, with a free version available (limited to 30 minute session at a time). The University of Washington Department of Chemistry lists other software options such as SpinWorks, and NMRPipe.


    .fq

    FASTA. Files can be opened in any text editor.

    .fsa

    Fragment analysis files. Can be opened with STRand Analysis Software (Windows only.)

    G

    .gdb

    ESRI geodatabase file (this is a directory of files)

    May be viewed in the open source software QGIS, for Mac, PC, Linux, Android, BSD.  Available at http://www2.qgis.org/en/site/

    To open in QGIS

    • Go to Layer -> add layer -> add vector layer
    • Under "source type", choose directory
    • Under source in the drop down menu, select OpenFileGDB
    • Click “Browse” to browse to the .gdb directory on your computer, select it and click "Open"
    • Click "Select All" to choose all layers
    • Click "Okay"

    .gds

    You can use R to access Genomic Data Structure (GDS) files, which have a .gds extension.

    • Start R then and install the gdsfmt package by entering the following at the R prompt:
    • Load the R package gdsfmt:
      • library(gdsfmt)
    • From within R, change the working directory to the directory where the .gds file is located by doing the following:
      • From the toolbar at the top of the screen, select “Misc”
      • From the pulldown, select “Change Working Directory”
      • Navigate to select the directory that contains the .gds file
    • From within R, type the following to open the .gds file, replacing yourFileName.gds with the name of your .gds file:
      • f <- openfn.gds("yourFileName.gds")
    • From within R, type the following to display the contents of the .gds file
    • From within R, type the following to close the GDS file 
      • closefn.gds(f)
    • From within R, type the following to do final clean up, replacing yourFileName.gds with the name of your .gds file:
      • cleanup.gds("yourFileName.gds")

    .geneious

    Geneious

    .gph

    Stata

    .gff

    Opens in TextEdit

    .gproj

    This is a GPlates project file. It should be located in a folder with other data files from the project, which have extensions such as .gpml, .rot, .gif, etc. Download (https://sourceforge.net/projects/gplates/?source=typ_redirect) and install GPlates, which is an open source application. From within GPlates, open the project (File->Open Project).

    .grd

    In conjunction with .gri file, this is a grid raster file.

    QGIS can be used to view a GRD file as follows:

    1. From within QGIS, go to the top navigation bar and select Layer > Add Raster Layer.

    2. On the resulting popup window, use the "Files of type" pull-down to select the one of the GRD types. Making this selection may involve a bit of trial and error.

    3. Navigate to the location of the GRD file, then select the file and press the Open button.


    A GRD file can also be opened in R. Load "raster", "sp", and "rgdal" packages, set your working directory, and load the raster file as an R object. E.g., for a grid file called EG_sample.grd

    • To work with rasters in R, two key packages are needed: sp and raster. If the packages are not installed, they must be installed.
    Install the raster package and sp, type the following in the RStudio console:
    install.packages('raster')
    Install the rgdal package by typing the following at the command line:
    install.packages('rgdal')
    • Load the raster, sp, and rgdal packages by typing the following in the RStudio console:
    library(raster)
    library(sp)
    library(rgdal)
    • To load the file, the following in the RStudio console where EG_sample is the name of the file and EG is a variable name:
    EG <- raster("EG_sample")
    • To view raster attributes, type the variable name you just loaded in the RStudio console. For example:
    EG
    • To plot the raster file, type the variable name you just loaded in the RStudio console. For example:
    plot(EG)

    For more detail, and further information, see Leah Wasser's (2015) tutorial at NEON Raster Data in R - The Basics.

    .gz

    Unarchiver (Mac only); also 7-zip will open these files

    Status

    Nonproprietary

    .gtx

    Genetix

    Program

    Genetix, opens in TextEdit

    H

    .hdr

    When associated with an .img file. NIfTI file for volumetric fMRI data (header and image data, stored either as one .nii file, or as an .hdr/.img pair). View with Chris Rorden's MRICron software at http://www.mccauslandcenter.sc.edu/mricro/ or with FreeSurfer software developed by the Martinos Center for Biomedical Imaging, Laboratory for Computational Neuroimaging, available at http://surfer.nmr.mgh.harvard.edu/ 

    .h5 (.hdf, .h4, .hdf4, .he2, .hdf5, .he5)

    Hierarchical Data Format. Can be opened with HDFView.

    I

    .ics

    Open source Image Cytometry Standard file. This may contain either header information/parameters only (if it is in conjunction with the image data as an .ids file), or it may contain both the header information and the binary image data in one file.  Files may be opened with freeware such as Fiji or ImageJ with the Bio-Formats plugin 

    .ids

    Open source Image Cytometry Standard file. Binary file with image data, in conjunction with a plain text .ics file which contains header information/parameters.  Files may be opened with freeware such as Fiji or ImageJ with the Bio-Formats plugin 

    .igs

    Initial Graphics Exchange Specification (IGES) format which stores computer-aided design (CAD) files.  Can be opened using freeware such as FreeCAD, which can be downloaded at http://www.freecadweb.org

    .img

    When associated with an .hdr file. NIfTI file for volumetric fMRI data (header and image data, stored either as one .nii file, or as an .hdr/.img pair). View with Chris Rorden's MRICron software at http://www.mccauslandcenter.sc.edu/mricro/ or with FreeSurfer software developed by the Martinos Center for Biomedical Imaging, Laboratory for Computational Neuroimaging, available at http://surfer.nmr.mgh.harvard.edu/ 

    .ims

    Imaris file format for large images. The simplest way to open these files is using ImageJ and it's plugin Bio-Formats package.

    .inp

    ArcGIS. These open with text editors.

    J

    .jar

    Java Archive (JAR) is a platform-independent file format that is used to zip multiple Java class files and associated metadata and resources (text, images, etc.) that are associated with a Java application/applet into a single file. A JAR file can be used to distribute application software or libraries on the Java platform. While JAR files usually contain compiled Java code (*.class), they sometimes also contain Java source code (*.java). The JAR format is based on the ZIP algorithm and mimics the Unix/Linux TAR file format in that JAR and TAR tools have the same command-line options.

    Following are a few basic commands for dealing with JAR files:

    • To view the contents of a JAR file: jar tf jar-file
    • To extract the contents of a JAR file: jar xf jar-file
    • To extract specific files from a JAR file: jar xf jar-file archived-file(s)
    • To run an application packaged as a JAR file (requires the Main-class manifest header): java -jar app.jar

    The following are good sites to learn the basics about JAR files:

    .jmp

    JMP file from SAS. Free 30 day trial for Mac or Windows available at JMP website. Or access in view only mode using the SAS Universal Viewer. Universal Viewer is available for Windows only.

    .jpg

    (Image file)

    Preview (Mac only)

    Ideal Format

    TIFF, JPEG2000

    .js

    This is a javascript file. To open: Open Notepad or TextEdit, open the template folder, then drag and drop the .js file into it.

    K

    .kml / .kmz

    KML (Keyhole Markup Language) is a form of XML notation used to express geographic information. A KML file shows geographic features such as place marks, images, polygons, 3D models and text descriptions. A KMZ file is a zipped file that contains one or more compressed KML files.

    The files can be viewed a couple of ways:

    L

    .LMD

    List mode data file. Flow Cytometry.

    .log

    Stata

    SAS

    .lsm

    .lsm file types are proprietary imaging files collected by Carl Zeiss microscopy software such as AIM or Zen.  These files can also be opened with freeware such as NIH ImageJ or Fiji

    M

    .m

    Matlab Opens in TextEdit

    .mas

    MEGA alignment session file. MEGA software available at http://www.megasoftware.net/index.php

    .mat

    Matlab

    R.matlab

    An alternative to using the Matlab application to access .mat files is to use Henrik Bengtsson's matlab package for R. If this is the first time you have used the R matlab package, you must first install it. (More information on the package is available at http://www.inside-r.org/packages/cran/R.matlab/docs/R.matlab.) To install the matlab package, open R  and type the following at the command line in the R console:

    install.packages("R.matlab")

    With the matlab package installed, load the matlab library by typing the following at the command line in the R console:

    library(R.matlab)

    From within R, change your working directory to the location of your Matlab file. (Click on "Misc" in the toolbar. Select "Change working directory" and navigate to the directory with your file.)

    Once you have updated your R working directory, load your Matlab file and assign it to a variable. We use "data" for our example, as shown below:

    data <- readMat('Your_matlab_data_file.mat')

    The data may be a list of lists. Type the following at the R command prompt:

    d1<-t(data[[1]][[1]])

    If the command completes successfully, type the following at the R command prompt to view the lists:

    d1 Once you have read the data file, you can also try to view the contents by typing the following at the command line in the R console:

    str(data)

    You may see output from the command in the R console. In this example, there are three variables (Y, X and Xs) and the output looks like this:

    List of 3
     $ Y : num [1:270555, 1:7] 1 2 3 4 5 6 7 8 9 10 ...
     $ X : num [1:299966, 1:10] 1 2 3 4 5 6 7 8 9 10 ...
     $ Xs: num [1:521074, 1:10] 1 1 1 1 1 1 1 1 1 1 ...
     - attr(*, "header")=List of 3
      ..$ description: chr "MATLAB 5.0 MAT-file, Platform: MACI64, Created on: Tue Oct 15 20:20:43 2013                                                 "
      ..$ version    : chr "5"
      ..$ endian     : chr "little"

    You can now view the values for each of the variables. For our example, you would type the following commands at thecommand line in the R console, pressing enter after each one: 

    data$Y
    data$X
    data$Xs

    NOTE: As of Feb 2017, R.matlab will not work for v 7.3 files (HDF5 schema). These may be viewed in John Eaton et al. software Octave or the HDF Group's software HDFView

    .mdb / .accdb

    A file with either of these extensions is an access database and can be accessed using Microsoft Access. The database can also be accessed using the MDB / ACCDB Viewer, which is available for a MAC (a free trial version that is fully functional except for export limitations) and as a Chrome web browser extension. The MDB / ACCDB Viewer for the MAC can be downloaded from http://eggerapps.at/mdbviewer/. The MDB / ACCDB Viewer Chrome extension is available from the Chrome Web Store at https://chrome.google.com/webstore/detail/mdb-accdb-viewer-and-read/mcfgopgpdlpcphkcijidlencdankpgbc?hl=en-US.

    .meg

    MEGA file. MEGA software available at http://www.megasoftware.net/index.php 

    .mgh

    4D neural imaging volume. Can be viewed using FreeSurfer software developed by the Martinos Center for Biomedical Imaging, Laboratory for Computational Neuroimaging. Available at http://surfer.nmr.mgh.harvard.edu/ 

    .mnb

    (Math Notebook)

    Adobe

    Wolfram CDF Player

    .mpk

    This is an ArcGIS Map Package, which is a compressed file that may have a geodatabase and/or shapefiles and/or other data. You should be able to open the .mpk file with a ZIP file utility like The Unarchiver to extract the components. Once you unpack those, you should be able to load them in QGIS or other applications as usual.

    .mts

    MEGA Tree session file. MEGA 6 software available at http://www.megasoftware.net/index.php. Files generated in MEGA 5 should be viewed in MEGA 5 (link to download MEGA 5 is available at http://www.megasoftware.net/knownissues.php)

    .mxd

    ArcGIS (PC Only)

    Available through UNC's Virtual Lab

    contact Phil McDaniel (GIS Librarian @ Davis for questions)

    philip_mcdaniel@unc.edu

    N

    .nas

    NASTRAN files generated by Strand7 software. These are plain text files that can be opened in any text editor. More reading here https://en.wikipedia.org/wiki/Nastran and http://www.strand7.com/.

    .nb

    Wolfram Mathematica notebook file. Can be viewed with MathReader, a free viewer from Wolfram Library Archive.

    .nc

    NetCDF (Network Common Data Form) file. Lots of tools available, handy java-based viewer Panoply (from NASA) at http://www.giss.nasa.gov/tools/panoply/ or Ncview from David W. Pierce at Scripps Institution of Oceanography at http://meteora.ucsd.edu/~pierce/ncview_home_page.html. See also the entry for netCDF.

    .nd2

    Nikon image file. May be opened with Nikon's NIS-Elements Viewer. There is also a plugin for ImageJ called Nikon ND2 Reader

    netCDF

    Unidata maintains a list of available softwares (both freely available and commercial) for viewing netCDF data. http://www.unidata.ucar.edu/software/netcdf/software.html

    Files in netCDF format can be opened using R as follows:

    If not installed, install the ncdf4 package:

    install.packages("ncdf4")

    If the ncdf4 package is installed, load the library and open the file as follows (replacing FILENAME with the actual name of the netCDF file.):

    library(ncdf4)

    data_ncdf <- nc_open("FILENAME")

    print(data_ncdf)

    .nex

    Nexus (ASCII)

    NeuroExplorer binary file. To read and write the NeuroExplorer [1] ‘.nex’ file format with Matlab or C++ (without NeuroExplorer.exe being installed), please refer to the downloads page [2] (‘Matlab code to read and write .nex files’ and  ‘C++ code to read and write .nex files’). ‘.nex’ files may furthermore be accessible through the neuroshare.dll (http://neuroshare.sourceforge.net).

    .nii

    NIfTI file for volumetric fMRI data (header and image data, stored either as one .nii file, or as an .hdr/.img pair). View with Chris Rorden's MRICron software at http://www.mccauslandcenter.sc.edu/mricro/ or with FreeSurfer software developed by the Martinos Center for Biomedical Imaging, Laboratory for Computational Neuroimaging, available at http://surfer.nmr.mgh.harvard.edu/ 

    MRICron only displays 2D & 3D files; for 4D files use FreeSurfer software from Martinos Center for Biomedical Imaging, Laboratory for Computational Neuroimaging. Available at http://surfer.nmr.mgh.harvard.edu/ 

    Another possible open source tool to access these files is Mango (http://ric.uthscsa.edu/mango/). The download site states that Mango, which is short for Multi-image Analysis GUI, is a viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes. The site has a tutorial and information for usage.

    NetLogo model file. May be viewed using NetLogo software. Wilensky, U. 1999. NetLogo.  http://ccl.northwestern.edu/netlogo/ . Center for Connected Learning and Computer-Based Modeling, Northwestern University. Evanston, IL.

    .npy

    Numerical Python

    Download NumPy from SciPy [3], a Python-based ecosystem of open-source software for mathematics, science, and engineering.


    import numpy as np

    np.load("path/to/file.npy")

    .nts

    Netsend Executable Text File. Opens in any text editor.

    .nxs

    Nexus (ASCII)

    .nwk

    Opens in textedit/notepad

    O

    .obj

    3D model file. Files can be opened with Open 3D Model Viewer (http://www.open3mod.com/ for Windows) or Tim Maxwell's OBJ Viewer (http://timmaxwell.org/pages/objviewer/ for Mac OS X). Another multiplatform option is Autodesk FBX Review.

    .odp

    OpenOffice Presentation

    .ods

    OpenOffice Spreadsheet

    .odt

    OpenOffice Text

    .opj

    Origin Project files. Origin Lab has a free software available for viewing Origin Project files (opj and older org) and Origin window files (ogg, ogw, ogm). The Origin Viewer is available for Mac and Windows https://www.originlab.com/viewer/

    P

    .pdf

    Portable Document Format

    Program

    Adobe

    Status

    Proprietary

    Ideal Format

    Text: .txt

    Graph: ???

    Image: .jpg

    .phy

    Source's collision model

    Can be viewed with text editor.

    .ply

    PLY is a computer file format known as the Polygon File Format or the Stanford Triangle Format. The format was principally designed to store three-dimensional data from 3D scanners. Wikipedia.

    PLY files can be opened with MeshLab.

    .plt

    Tecplot PLT binary format. This format is Tecplot’s traditional format and is commonly exported by solvers. [2]

    Can also view .plt files with Paraview

    .pkl

    pickle — Python object serialization [1]

    ASCII files. Can be opened in a text viewer.

    .pse

    Molecular model image

    Program

    PyMOL

    Status

    Proprietary (but much of it is open source)

    .psd

    Photoshop Document

    A psd  is a layered image file used in Adobe PhotoShop.

    Can be opened with the freePSD Plugin + Paint.NET

    .pzf (.pzfx, .pzm, .pzt)

    Prism files. Can be opened with the free Prism file viewer.

    Q

    .qgd

    Shimadzu instrument data format files (proprietary). May be viewed in OpenChrom®(open source software for chromatography and mass spectrometry) available at https://www.openchrom.net/home. To open .qgd files you will need the Shimadzu QGD import converter. Click on "plug-ins" and in the drop down menu click on "marketplace".

    R

    .r

    R

    Can be opened in TextEdit

    .rar

    for Mac: UnRarX http://unrarx.en.softonic.com/mac

    for PC: 7zip http://www.7-zip.org/

    .raw/.RAW

    Files with the extension .raw (or .RAW) can be of a number of different types. Sometimes, even though you can't read most of the file, you may be able to open the file with a plain text editor and spot some clues as to which type of file you are dealing with. For example, if you can see the word "Finnigan" in the file, it may be output from a Finnigan Mass Spectrometer. That will let you know that you might want to try something like OpenChrom to open the file.

    A few possible types of .raw files are shown below:

    • A .raw file may be simply a plain text file that can be opened with a text editor such as TextEdit.
    • A .raw file may be a genome file that can be opened with the program PLINK.
    • A .raw file that is compatible with Thermo Xcalibur, Micromass MassLynx, and Perkin Elmer TurboMass, can be opened using tools from ProteoWizard. First open the MSConvert GUI. Browse to find the file(s) to open and select the file(s) to Add to the top left pane in the GUI window. Select the Output format mzML, and them click on the Start button to convert the file to one with the extension .mzML. Open the folder with the .mzML file(s). Right click on the .mzML file and select SeeMS to open the file in the SeeMS GUI.
    • A .raw file might be an image file.

    .rdata (or .rda)

    This file contains R data. It is not readable in a text editor like TextEdit or Notepad. To open an RData file in RStudio, do the following:

    • Open the RStudio application
    • From the top navigation bar, select Session -> Set Working Directory -> Choose Directory
      • Navigate to the directory containing the RData file(s) and press the "Open" button on the bottom right of the window.
    • A list of the files in the directory you just selected should now be displayed in the "Files" pane in RStudio, and you should see the RData file in that list.
    • From the "Files" pane in RStudio, click on the RData file and when asked to "Confirm load RData," click "Yes".
      • You should now see content from the RData file in the "Environment" pane of RStudio.
    • You may be able to do a preliminary check of the data listed in the "Environment" pane by clicking on the circle next to any listed content to expand and contract
    • In the "Console pane" of RStudio, type the following to examine the contents of the RData file:
      • ls() to view all objects (tables) in the R database
      • head(OBJECTNAME) to view information in the first parts of the object.
      • names(OBJECTNAME) to view the labels (column headings) in a specific object (table), where OBJECTNAME is the name of an object discovered while using ls()
      • OBJECTNAME$COLUMNNAME to view all the data in a single column
      • Depending on how the structure of the data, there are two possible ways to view all the strings of data present in a given object (table).
        • Try str(OBJECTNAME).
        • If str() does not work, try names().

    See https://www.statmethods.net/input/contents.html for some useful functions for listing the contents of an object or dataset.

    .rds

    A file with the .rds extension stores an R object. It is not readable in a text editor like TextEdit or Notepad. To open the file, do the following:

    1. Open R

    2. At the R command prompt, type the following to read the .rds file into the variable x:

               x <- readRDS("YourFileName.rds")

    3. Type the following at the R command prompt to view the contents of the .rds file, which has been assigned to the variable x:

               x

    .rtf

    Rich text format

    S

    .sam

    SamTools

    .BAM is the binary version of .SAM. We prefer SAM because it is a tab-delimited text file and easily readable.

    .sas

    SAS

    Can be converted using StatTransfer (available at https://www.stattransfer.com)

    .sas7bdat

    A .sas7bdatfile is a binary database storage file created using SAS software. The file can be accessed using R.

    To open/view the .sas7bdat files, do the following from within R:

    1. Set your working directory to the directory containing the .CEL files by typing the following in the R console:
    setwd("your full directory here with quotation marks")
    2. Install the ‘sas7bdat’ package and load the library by typing the following in the R console:
    install.packages("sas7bdat")
    library(sas7bdat)

    3. Read in the data by typing the following in the R console:
    s7bdatfile <- read.sas7bdat("/Users/Debra/Desktop/newkoweps_fn.sas7bdat")
    4. Begin inspecting the data by typing the following in the R console:
    View(s7bdatfile)

    .sav

    SPSS file

    PSPP software is an open source alterative for viewing, available at http://www.gnu.org/software/pspp/

    OR

    Open in R

    An alternative to using the Stata or the StatTransfer application to access .dta files is to use R. Open R  and load the "foreign" library by typing the following at the command line in the R console:

    library(foreign)

    From within R, change your working directory to the location of your .dta file. (Click on "Misc" in the toolbar. Select "Change working directory" and navigate to the directory with your file.)

    Once you have updated your R working directory, load your .dta file and assign it to a variable. We use "data" for our example, as shown below:

    data<-read.spss("Your_data_file.sav")

    Once you have read the data file, you can view the contents by typing each of the following commands at the command line in the R console, pressing enter after each one: ls()                 to view all objects (tables) in the R database

    str(data)            to view the labels (column headings) in an object (table) from the ls() command (may not work in some databases)

    names(data)          to view the labels (column headings) in an object (table) from the ls() command (may not work in some databases)

    data$COLUMNNAME      to view all the data in one of the single columns for column headings shown form the command above

    .sbfmf

    Static Background Fly Movie Format (SBFMF) is a compressed video format. You can use the Ctrax application to view the video.

    1. Install the Ctrax application.
      1. Go to the following instructions at:  http://ctrax.sourceforge.net/install.html#ctrax-installation
      2. Go to the section labeled Ctrax Installation and locate your platform (Windows, Mac or Ubuntu). Click on the link to go to the Windows Installer, Mac OS X Installer or the Ctrax PPA Repository (for Ubuntu). Follow the instructions to download and install.
    2. Once it is installed, click on Ctrax to open the application.
    3. Select File and then Open. Navigate to the location of the .sbfmf file(s). Select the file you want to open and press the Open button. A pop-up window will ask you to “Choose annotation file.” If you see the name of the .sbfmf file prefilled in the Save As field, change the file extension to .ann (or to any other extension besides .sbfmf) and press the Save button.
    4. A viewer with a still frame from the video should open.
    5. Press the arrow on the bottom toolbar to play the video. 

    .sf

    Salmon quantification file. Plain text, TSV. Should be present with a directory called aux_info with a JSON metadata file and various parameter files. See more information at the Salmon Output File Formats page

    .sf3

    Scaffold file for proteomics data - can be opened using the Proteome Software Scaffold free viewer (http://www.proteomesoftware.com/products/scaffold/download/).

    .sff

    Standard flowgram format. 

    NextGen Workbench at http://www.dnabaser.com/download/nextgen-fastq-editor/index.html or BAMseek at http://www.dnabaser.com/download/nextgen-fastq-editor/index.html

    .shp

    Shapefile

    A shapefile is an open format collection of files used to store GIS data. Shapefiles must have at least three basic files present in the same directory: .shp (main file), .shx (header) and .dbf (database file). Shapefiles may also include additional files with the following extensions: .atx, .sbn, .sbx, .fbn, .fbx, .ain, .aih, .ixs, .mxs, .prj, .xml, .cpg, lyr. Two good sources for more info on shapefiles and GIS are https://www.gislounge.com/shapefile-viewers/ and https://docs.qgis.org/2.18/en/docs/gentle_gis_introduction/index.html.

    You can view shapefiles by opening the main file (.shp) using the GUI for QGIS, which is open source and available for Windows, MacOS X, Linux and Android at http://www2.qgis.org/en/site/.

    Shapefiles can also be viewed using ArcGIS (available for Dryad curators through UNC's Virtual Lab. Contact Phil McDaniel, GIS Librarian @ Davis, philip_mcdaniel@unc.edu).

    To view on ArcGIS (PC only):

    To open

    • Run ArcCatalog through VirtualLab.
    • Connect to folder containing the shp (and related) files.
    • Concatenated shape file or maps should appear in the directory in the left pane.
    • Use the preview function in the right pane to view.

    .smcl

    Stata

    (Alternate extension for .log files)

    .spf

    Sequencher project file. Proprietary to Gene Codes Corporation at http://www.genecodes.com

    .spm

    FemtoScan scanning probe microscopy (SPM) file. The company FemtoScan does make available a 30 day free trial version of the software needed to visualize these files. Windows only. You might also try Gwyddion, which is an open source software for SPM data visualization and analysis (available for linux, Mac, Windows) developed by Department of Nanometrology, Czech Metrology Institute.

    .spv

    SPSS

    The .spv extension denotes a compressed data file that contains output generated from data analytics functions run within SPSS software. The file may store datasets, reports, charts, and other visualizations. It can be opened/viewed using SPSS by choosing the following from the top navigation bar:

    File --> Open --> Output.

    It may also be viewed in IBM® SPSS® Smartreader. Link to download available [here] under "The Smartreader" heading. Registration required.

    Can also be converted using StatTransfer

    .sqlite

    This is a database file. It can be opened using R and the package RSQLite.

    1. Load the RSQLite package in RStudio by entering the following in the console:

    install.packages("RSQLite") # NOTE: Skip if RSQLite installed previously. Try to load the library to check.
    library("RSQLite")

    2. Connect to the sqlite file. Enter the following in the console replacing "myFile.sqlite" with the name of the file you are checking.

    sqlite   <- dbDriver("SQLite")
    testdb <- dbConnect(sqlite,"myFile.sqlite")

    3. List the tables in the database

    dbListTables(testdb)

    4. To view each of the tables, enter the following in the console replacing tableName with the name of the table you want to view:

    dbReadTable(testdb, "tableName")

    .stl

    3D Imaging

    To Open

    Use Pleasant 3D on Mac

    Alternatively, MeshLabs is free, open-source software available at http://meshlab.sourceforge.net/ for any OS.

    .st7

    3D models

    To Open

    Strand7 Viewer software: available for free download at http://www.strand7.com/html/viewer.htm

    .sud

    Audacity

    A .sud file may be an audio file, and it may be imported into Audacity as a raw file: File > Import > Raw Data.

    .sylk

    Opens using Notepad

    T

    .tbl

    Opens in TextEdit

    .tar

    7zip (PC only)

    The Unarchiver (Mac only)

    TAR (*nix)

    Status

    Nonproprietary

    .tar.gz

    7zip (PC only)

    Unarchiver (Mac only)


    If you need to check a number of large files in a Linux or Mac environment, especially ones located in subdirectories, you can adapt the following shell script. Create a file with a .sh extension that has the following content, and set permissions to make it executable. For example, to make script.sh executable, issue the following command: chmod 0755 script.sh or chmod +x script.sh. Just be sure to update file paths/names to reflect your files:

    #!/bin/sh
    # Update the path to reflect the location and file name for your output file 
    > /dryad-data/InCuration/Underhill/head_out.txt
    
    # Loop through all '*.fastq.gz' files in the current directory and all subdirectories
    find . -type f -name '*.fastq.gz' -print | while read FILE
    do
        # Print the file name to the screen and to the output file
        echo $FILE
        echo "=============================" >> /dryad-data/InCuration/author/head_out.txt
        echo $FILE >> /dryad-data/InCuration/author/head_out.txt
        echo "=============================" >> /dryad-data/InCuration/author/head_out.txt
        echo "" >> /dryad-data/InCuration/author/head_out.txt
    
        # Print the first 10 lines of the '*.fastq.gz' file to the output file
        zcat $FILE | head >> /dryad-data/InCuration/author/head_out.txt
        echo "" >> /dryad-data/InCuration/author/head_out.txt
        echo "=============================" >> /dryad-data/InCuration/author/head_out.txt
    done
    


    Status

    Nonproprietary

    .tbz

    Variant of .tar.gz

    Program

    7zip (PC only)

    Unarchiver (Mac only)

    Status

    Nonproprietary

    .tbz

    Variant of .tar.gz

    Program

    7zip (PC only)

    Unarchiver (Mac only)

    Status

    Nonproprietary

    .tdsm

    Data file saved in the National Instruments (NI) Technical Data Management Streaming (TDMS) format. It contains simulation or measurement data recorded by National Instruments software, such as LabVIEW and DIAdem.

    Program

    TDM Excel Add-In (http://www.ni.com/example/27944/en/) MATLAB (http://www.ni.com/example/30957/en/) Python

    Status

    Proprietary

    .tif

    TIFF (Tag Image File Format)

    Can be opened with:

    .tnt

    Super Matrix

    Can be opened in textedit/notepad

    .tped

    View in notepad

    .txt

    Text file

    Status

    Nonproprietary

    Ideal Format

    .txt

    .tre

    NEXUS tree file

    Program

    TreView

    Opening

    Can be opened in TextEdit/Notepad

    U

    V

    .vaxml

    Virtual Anatomy eXtensible Markup Langauge (VAXML) format which, when used in conjunction with a set of .stl (STereoLithography) files, is used to build 3-D CAD models.  Can be opened using freeware such as SPIERSview , which can be downloaded at http://www.spiers-software.org

    .vcf

    Variant Call Format. 

    vcf is useful for very large files, and for manipulating them, but the format is plain text so they can also open in any text editor - for large files, just drag and drop into Notepad++

    Program

    Integrative Genomics Viewer (IGV) at http://www.broadinstitute.org/igv/VCF This is an open source viewer that can be used to view Variant Call Format (.vcf) files. To load the .vcf file, Go to the top navigation bar, and from the pull-down for "File", select "Load from File..." Navigate to and select the file you are loading.

    SamTools at http://www.htslib.org

    VCFTools available at http://vcftools.sourceforge.net.

     BAMseek at https://code.google.com/p/bamseek/


    W

    .wdq

    WinDaq-acquired data file. Proprietary. Free viewer, WinDaq Waveform Browser, available from DATAQ Insturments at http://www.dataq.com/products/windaq/#nested-tab-3

    .wiff

    Program

    AB Sciex Analyst (Mass Spectrometery software)

    Ideal Format

    MzML

    Conversion Instructions

    To convert from .wiff to MzML (xml format), download and install AB SCIEX MS Data Converter, available here: [4]. Note: for PCs only.

    Create text file containing the text:

    AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]

    Pause

    Here is an example version:

    AB_SCIEX_MS_Converter WIFF "C:\Users\rwalton\Downloads\T superba Male - Raw LDI\T superba Male - Raw LDI\2013 - 2 days old T superba Male 02 Osmeterium - Redone.wiff" -profile MZML "C:\Users\rwalton\Desktop\wiffconversion.xml" /nocompression /index

    Pause

    Replace the file paths contained in the quotation marks with the input file and the export file (that you will create through the conversion process). When you have the command prompt written, save the text file. Name this file something that will help you remember what it is such as "conversion," and save this file as a .bat (batch) file instead of a text file. Drag and drop the file from wherever you saved it into the AB SCIEX MS Converter's program folder (C:\Program Files (x86)\AB SCIEX\MS Data Converter). You will be prompted to accept Administrator privileges to do this. Once the file is in the program folder, double click it to run the batch file. A terminal/command line box will appear. If you get no error messages in that box, then check the location you saved the output file. You should have an xml file containing the wiff data.

    .wsp

    Program

    FlowJo

    X

    .xls

    Spreadsheet

    Program

    Microsoft Excel (1997-2003)

    Status

    Proprietary

    Ideal Format

    .csv, ASCII

    .xlsx

    Spreadsheet

    Program

    Microsoft Excel (2007-)

    Status

    Nonproprietary, patented

    Ideal Format

    .csv

    .xml

    These can be read with a text editor. If they do not open, you can click 'view' to see the contents.

    Y

    Z

    .zip

    Compressed file(s)

    Program

    7zip (PC only)

    Unarchiver (Mac only)

    Status

    Nonproprietary, patented

    .zip.001, .zip.002, ...

    Created by using archiving software to split a large zip file into volumes. Each volume has the same maximum size, and once that size is reached for the first volume file a new volume file is created. This process continues until all of the data has been compressed. Even though the zip file is split into smaller files, it is still technically a single zip archive and not five individual zip files. You need all the files to unzip the archive. You only unzip the first volume (the one ending in .zip.001), and your zip program recombines the volumes and unzips everything at once.

    Program

    7zip (PC only)

    Keka File Archiver Utility (Mac only)