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  • coveragebed output result problem

    Hi,

    I'm running coveragebed to calculate the number of read count in each transcript of tophat alignment result by using the following command:
    Code:
    /bedtool/arq5x-bedtools-26a87ab/bin/coverageBed -abam accepted_hits.bam -b transcripts.bed > transcripts.cov.txt 
    cat transcripts.cov.txt
    gi|224589800|ref|NC_000001.10|  8378168 8404227 "ENSG00000162426"       [B]70      1059    26059   0.0406386[/B]
    Does anybody knows what is the 70, 1059, 26059, 0.0406386 represent?
    I know that 0.0406386 is obtained from 1059/26059.
    Is it 1059 refer to total number of read aligned to the transcript and 26059 represent the transcript length? How about 70?
    Kindly correct me if I'm wrong.
    Thanks for any advice.

  • #2
    If you type "coverageBed -h", the last few lines describe the output format.

    Code:
    Default Output:  
    	 After each entry in B, reports: 
    	   1) The number of features in A that overlapped the B interval.
    	   2) The number of bases in B that had non-zero coverage.
    	   3) The length of the entry in B.
    	   4) The fraction of bases in B that had non-zero coverage.

    Comment


    • #3
      Was looking for this detail

      Thanks alot , very much helped.

      Comment

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