featureCounts assigning reads criteria
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Entering edit mode
8 weeks ago

I know by default, featureCounts does not count multi-mapping reads. My question is, by default, does featureCounts try to assign the following, or automatically categorize as unassigned?

  • singletons (i.e., only one mate is mapped for paired-end reads)
  • non-properly paired reads (i.e., both mates mapped, but not necessarily properly paired/in proper orientation)
featureCounts • 115 views
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