coverageBed question

[jlfmssm]

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]

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]

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:

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):

coverageBed -ibam 1382_1_sorted.bam -b hg18.bed.sorted  > hg18_seq.cov.txt

I hope this helps,
Aaron