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

jmartin · 04-18-2018, 03:15 PM

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.

GenoMax · 04-19-2018, 05:19 AM

Use mosdepth and option --by 10000.

You can also use deepTools and option multiBamSummary bins.

Mizzou55 · 04-19-2018, 11:36 AM

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

jmartin · 04-19-2018, 02:19 PM

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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04-18-2018, 03:15 PM	#1
jmartin Member Location: St. Louis Join Date: Dec 2009 Posts: 74	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.

04-19-2018, 05:19 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	Use mosdepth and option --by 10000. You can also use deepTools and option multiBamSummary bins.

04-19-2018, 11:36 AM	#3
Mizzou55 Junior Member Location: st. louis Join Date: Mar 2010 Posts: 7	Does the --by option sum up the coverage for an interval (10000), or does it provide the depth at each interval?

04-19-2018, 02:19 PM	#4
jmartin Member Location: St. Louis Join Date: Dec 2009 Posts: 74	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