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  • Need simple way to get coverage per 10kb interval on reference

    Is there a tool that can tell me coverage per some uniform interval along a set of reference contigs? I know I could use bedtools coverage and build a bed file defining the intervals, but I was asked if there wasn't already a tool that could just do uniform intervals on its own without having to setup a bedfile to define the intervals.

  • #2
    Use mosdepth and option --by 10000.

    You can also use deepTools and option multiBamSummary bins.

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    • #3
      Does the --by option sum up the coverage for an interval (10000), or does it provide the depth at each interval?

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      • #4
        Thanks for the suggestion, mosdepth is just what I need!

        @Mizzou55 it looks like its reporting the average depth across the requested intervals. If you want depths at specific positions in your reference I guess you'd have to setup a bed file with the positions you want reported

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