Mean Coverage version of stat_coverage and coverage?

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gen ▴ 30

@gen-7383

Last seen 9.1 years ago

United States

Hi, I've been using coverage(GRangesList) and stat_coverage(GRangesList) for read coverage but is there a function to get mean coverage and a mean graph for several different GRangesLists? When I calculate coverage I would like to specify a beginning and ending position for each GRangesList so that each one will have a comparable range to each other. Or is it a better idea to just subset the GRangeList directly?

Thanks

grangeslist granges Genomicfeatures bam • 1.2k views

ADD COMMENT • link 9.2 years ago gen ▴ 30

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If there is no equivalent to stat_coverage or coverage that can average several inputs. Would it be possible to possible to maybe 'average' the GRangeLists themselves? IE put them in equal sized bins and then for each position count how many reads cover that position and then divide it by the number of inputs?

ADD REPLY • link 9.2 years ago gen ▴ 30

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