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  • coverageBed

    Hi,

    Could someone please tell me which column of the output file from "coverageBed" is the number of the raw read count for each gene? Actually, I do not understand the explanation in the protocol.
    -------------------------------------------------------------------------------------
    Default Output of coverageBed:
    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.
    -------------------------------------------------------------------------------------

  • #2
    If A is the reads and B is the genes, then the last four columns will be # reads per gene, # bases of the gene with reads overlapping them, length of gene, and fraction of gene with reads.

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