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Old 04-11-2019, 07:23 AM   #2
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Join Date: Feb 2008
Posts: 7,059

Not sure what exactly you are asking. One feeds featureCounts with files that are already aligned. featureCounts only does counting.

Note: featureCounts is part of a larger package called "subread". subread is an aligner that can be used to create BAM files by alignment.
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