Difference between revisions of "Opening Files"

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Integrative Genomics Viewer (IGV) at [http://www.broadinstitute.org/igv/VCF http://www.broadinstitute.org/igv/VCF]
 
Integrative Genomics Viewer (IGV) at [http://www.broadinstitute.org/igv/VCF 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 http://www.htslib.org]
 
SamTools at [http://www.htslib.org http://www.htslib.org]

Revision as of 07:09, 21 April 2015

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.

Contents

A

.ale

Avid (ASCII)

.am

Amira files. Proprietary. 

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/.

C

.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

D

.dat

Matlab

.dcm

DICOM file. For Mac, may use OsiriX image processing software to view, available at http://www.osirix-viewer.com

.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

E

.eps

(Encapsulated PostScript Image File) Preview

F

.faa

FASTA

.fas

FASTA

.fasta

FASTA

.fastq

FASTA

.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

.fdi

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

.fq

FASTA

G

.geneious

Geneious

.gph

Stata

.gff

Opens in TextEdit

.gz

Unarchiver (Mac only)

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/

I

.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/

.inp

ArcGIS

J

.jpg

(Image file)

Preview (Mac only)

Ideal Format

TIFF, JPEG2000

K

L

.LMD

List mode data file. Flow Cytometry.

log

Stata

SAS

M

.m

Matlab Opens in TextEdit

.mas

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

.mat

Matlab

.meg

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

.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

.nc

NetCDF (Network Common Data Form) file.

.nex

Nexus (ASCII)

.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/

.npy

Numerical Python

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

.nxs

Nexus (ASCII)

.nwk

Opens in textedit/notepad

O

.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

.pse

Molecular model image

Program

PyMOL

Status

Proprietary (but much of it is open source)

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

UnRarX

.rdata (or .rda)

R

Not readable in TextEdit

Further Instructions

Open in R

Use the following functions to view more information:

  • 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
  • str(OBJECTNAME) to view all strings of data present in a given object (table)

Try both names() or str() because for some databases, only one will work (unsure as to why).

.rtf

Rich text format

.raw

Genome file

Program

PLINK

can also be opened in TextEdit


May also be an image file.

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)

.sav

SPSS file

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

.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

ArcGIS (PC only)

(should be present with .dbf, and .shx files of same name to open in ARCviewer or ARCcataloger, .prj is optional file) Available through UNC's Virtual Lab contact Phil McDaniel (GIS Librarian @ Davis for questions) philip_mcdaniel@unc.edu

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

May 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

T

.tbl

Opens in TextEdit

.tar

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary

.tar.gz

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary

.tgz

Variant of .tar.gz

Program

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary

.tnt

Super Matrix

Can be opened in textedit/notepad

.txt

Text file

Status

Nonproprietary

Ideal Format

.txt

.tre

NEXUS tree file

Program

TreView

Opening

Can be opened in TextEdit/Notepad

U

V

.vcf

Variant Call Format. 

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

Y

Z

.zip

Compressed file(s)

Program

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary, patented