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Old 07-01-2010, 02:58 AM   #3
quinlana
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Location: Charlottesville

Join Date: Sep 2008
Posts: 119
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Quote:
Originally Posted by jlfmssm View Post
I try to run coverageBed like this:
/home/ay55/BEDTools/bin/genomeCoverageBed -ibam 1382_1_sorted.bam -i hg18.bed.sorted -g hg18.genome > hg18_seq.cov.txt

no error at all, but when I open hg18_seq.cov.txt, I got this
read block failed - CheckBlockHeader() returned false
Could not read header type

Any idea?
Assuming you want to run genomeCoverageBed (chromosome level coverage), you would do so as follows:

Code:
genomeCoverageBed -ibam 1382_1_sorted.bam  -g hg18.genome > hg18_seq.genomecov.txt
If you want to run coverageBed (coverage across intervals defined in a BED file):

Code:
coverageBed -ibam 1382_1_sorted.bam -b hg18.bed.sorted  > hg18_seq.cov.txt
I hope this helps,
Aaron
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