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Old 04-18-2018, 02:15 PM   #1
jmartin
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Default 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.
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Old 04-19-2018, 04:19 AM   #2
GenoMax
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Use mosdepth and option --by 10000.

You can also use deepTools and option multiBamSummary bins.
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Old 04-19-2018, 10:36 AM   #3
Mizzou55
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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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Old 04-19-2018, 01:19 PM   #4
jmartin
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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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