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-   -   coverageBed question (http://seqanswers.com/forums/showthread.php?t=5734)

jlfmssm 06-28-2010 09:11 PM

coverageBed question
 
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?

zee 06-28-2010 11:39 PM

I dont think you are giving the program the correct options.

You should only one of either

BAM file as input "-ibam"
or
BED file as input "-i"

quinlana 07-01-2010 02:58 AM

Quote:

Originally Posted by jlfmssm (Post 20991)
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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