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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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Extend nucleotides to be counted on bamCoverage "--MNase" argument. #992

Open chesterlee7246 opened 4 years ago

chesterlee7246 commented 4 years ago

Hi, bamCoverage "--MNase" is a good argument, but it only counts 3 nucleotides at the center of each fragment. Is it possible to add another argument to specify an offset with respect to fragment center, such as "-30,30", means counts 60 bp at the center of each fragment. Thanks!

LeilyR commented 4 years ago

I wonder if using --centerReads along with --Offset and --minFragmentLength/--maxFragmentLength would already give you your desired output.