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Title:	File Formats
Author:	Nowlan Freese	Mar 26, 2015
Last Changed by:	Paige Kulzer	Apr 24, 2024
Tiny Link: (useful for email)	https://wiki.bioviz.org/confluence/x/NAAN
Export As:	Word · PDF

IGB User's Guide (2)     Page: I can't see my data     Page: Reference sequence

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Time	Editor
Apr 24, 2024 14:05	Paige Kulzer	View Changes
Updated USeq documentation to confirm it is only available in IGB 9.1.8 and earlier.
Mar 27, 2024 12:39	Paige Kulzer	View Changes
Added row to table with information about the CRAM file format; fixed several broken links throughout the table
Dec 21, 2015 14:01	Ann Loraine	View Changes
Dec 21, 2015 14:00	Ann Loraine	View Changes
Dec 21, 2015 14:00	Ann Loraine

External Links (24)
    www.biostat.jhsph.edu/~hji/cisgenome/
    www.sanger.ac.uk/Software/formats/GFF
    https://bitbucket.org/lorainelab/affyprobesetsforigb
    useq.sourceforge.net
    samtools.sourceforge.net
    www.biodas.org/documents/spec.html
    https://wiki.bioviz.org/confluence/display/igbman/About+ann…
    https://github.com/samtools/hts-specs
    genome.ucsc.edu/goldenPath/help/customTrack.html#PSL
    genome.ucsc.edu/FAQ/FAQformat#format1
    www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
    samtools.sourceforge.net/tabix.shtml
    genome.ucsc.edu/FAQ/FAQblat.html
    genome.ucsc.edu/goldenPath/help/bigBed.html
    genome.ucsc.edu/FAQ/FAQformat.html#format7
    biodas.org/documents/das2/das2_protocol.html
    genes.cs.wustl.edu/GTF2.html
    genome.ucsc.edu/goldenPath/help/wiggle.html
    https://wiki.bioviz.org/confluence/pages/viewpage.action?pa…
    genome.ucsc.edu/goldenPath/help/customTrack.html#GTF
    song.sourceforge.net/gff3-jan04.shtml
    genome.ucsc.edu/goldenPath/help/bigWig.html
    www.biostat.jhsph.edu/~hji/
    www.biodas.org

IGB User's Guide (2)     Page: Sharing data for a custom genome not already part of IGB QuickLoad     Page: Visualizing probe sets