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bamCoverage [multiBamCoverage] #1313

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z5ouyang opened this issue May 11, 2024 · 1 comment
Open

bamCoverage [multiBamCoverage] #1313

z5ouyang opened this issue May 11, 2024 · 1 comment

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@z5ouyang
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If I have multiple bam files (replicates), how bamCoverage work?
There used to be a function multiBamCoverage but it has been removed from the latest deeptools (3.5.5).
How do you suggest to merge those bam files, if bamCoverage can only work on a single bam? This might be related to #1195, some merged method might not work with bamCoverage?

Thanks!
@WardDeb
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WardDeb commented May 27, 2024

If you need bws / bedgraphs you can run bamCoverage separately for all bam files.
The functionality for multiBamCoverage can be found in multiBamSummary.

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@WardDeb @z5ouyang