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Old 02-22-2013, 12:40 PM   #1
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Join Date: Feb 2013
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Default 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.

hari_iyer16 is offline   Reply With Quote

coveragebed, galaxy, genomecoveragebed

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