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  • hari_iyer16
    Junior Member
    • Feb 2013
    • 8
    #1

    Using coverageBed in Galaxy

    Hi, I am new to Galaxy. I want to compute the sequencing tag coverage in defined intervals (like 0-99 bp, 100-199 bp, 200-299 bp ...) across all chromosomes from a ChIP-seq data, which is in the BED file format (with fields Chromosome, Start, End). BEDTools has the command "coverageBed" to do this. Is it possible to compute what want in Galaxy? In Galaxy I could find "Create a BedGraph of genome coverage" which computes the genome-wide coverage of intervals defined in a BAM or BED file, not in user-defined intervals. I think what Galaxy offers is "genomeCoverageBed" from BEDTools.
    I appreciate any help.

    Sincerely.
    Tags: coveragebed, galaxy, genomecoveragebed
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