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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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bamCoverage [multiBamCoverage] #1313

Open z5ouyang opened 6 months ago

z5ouyang commented 6 months ago

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 commented 6 months ago

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