Difference between revisions of "Opening Files"

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How to change a PC's default settings for opening files: 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.
 
How to change a PC's default settings for opening files: 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.
  
A resource to learn about a particular file type and find the right program to open it is www.openthefile.net/.
+
A resource to learn about a particular file type and find the right program to open it is http://www.openthefile.net/.
  
 
= A =
 
= A =

Revision as of 06:15, 15 June 2017

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.

This list is alphabetical by file extension.

Several of these programs can be used through UNC's Virtual Lab found here

For lists of nonproprietary formats based on data type, see this wikipedia article.

For summary of file formats based on file type, see here.

How to change a PC's default settings for opening files: 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.

A resource to learn about a particular file type and find the right program to open it is http://www.openthefile.net/.

Contents

A

.ab1

Chromatogram files. Can be opened with 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

.abf

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

.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.

.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 conisists 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.).

.biom

Biological Observation Matrix format

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 using CRAMTools software or Samtools 

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>

.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]

Status

Nonproprietary

Ideal Format

.csv

.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

Stata

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

OR

Stata - 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.dta("Your_data_file.dta")

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

.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.

.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, open R and type/copy the following into the R console to install the packages (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.):  

source("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]

.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. Can 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

  • Load the file: EG <- raster("EG_sample")
  • To view raster attributes: EG
  • To plot the raster file: 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

.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

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

.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

.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/.

.nc

NetCDF (Network Common Data Form) file. Lots of tools available, handy java-based viewer at http://www.giss.nasa.gov/tools/panoply/

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

.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/ 

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

P

.pdf

Portable Document Format

Program

Adobe

Status

Proprietary

Ideal Format

Text: .txt

Graph: ???

Image: .jpg

.phy

Source's collision model

.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 the file, do the following:

  • ls() to view all objects (tables) in the R database
  • 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().

.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. 

.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

Must be present with .dbf (database file) and .shx (header) files of the same prefix to open in ARCviewer or ARCcataloger. May also be present with optional  .prj (projection file) and .lyr (layer file) and other index files. Available through UNC's Virtual Lab contact Phil McDaniel (GIS Librarian @ Davis for questions) philip_mcdaniel@unc.edu

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 the the directory in the left pane.
  • Use the preview function in the right pane to view.

QGIS is an open source alternative, for Mac, PC, Linux, Android, BSD.  Available at http://www2.qgis.org/en/site/

.smcl

Stata

(Alternate extension for .log files)

.spf

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

.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

.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)

Status

Nonproprietary

.tbz

Variant of .tar.gz

Program

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary

.tgz

Variant of .tar.gz

Program

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary

.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.

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)