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  • 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?

  • #2
    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"

    Comment


    • #3
      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

      Comment

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