What is the behavior of quasimapping when reads overlap multiple transcripts?

COMBINE-lab / RapMap

Rapid sensitive and accurate read mapping via quasi-mapping

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What is the behavior of quasimapping when reads overlap multiple transcripts? #42

Open nachocab opened 6 years ago

nachocab commented 6 years ago

I haven't been able to find a clear answer in the documentation: are the read counted as in all the transcripts they overlap or are they divided amongst them. If it's the second case, is it kosher to add the counts for all the transcripts of a given gene to get the "gene counts"?