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Old 01-23-2011, 03:37 PM   #1
jay2008
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Location: Australia

Join Date: Sep 2010
Posts: 44
Default bam to coverage

Hello,
I tried to get coverage from BAM file in the following format:
chr strand chrom_start chrom_stop count
chr1 + 287 293 3
chr1 + 294 200 8
chr1 + 201 205 1
chr1 - 290 295 5
...

I can use genomeCoverageBed as blow
genomeCoverageBed -bg -ibam *.bam -g chr.size -strand + > pos.txt
genomeCoverageBed -bg -ibam *.bam -g chr.size -strand + > pos.txt

then put them together.
do you know a simpler way?

jian
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