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  • bam to coverage

    Hello,
    I tried to get coverage from BAM file in the following format:
    chr strand chrom_start chrom_stop count
    chr1 + 287 293 3
    chr1 + 294 200 8
    chr1 + 201 205 1
    chr1 - 290 295 5
    ...

    I can use genomeCoverageBed as blow
    genomeCoverageBed -bg -ibam *.bam -g chr.size -strand + > pos.txt
    genomeCoverageBed -bg -ibam *.bam -g chr.size -strand + > pos.txt

    then put them together.
    do you know a simpler way?

    jian

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