RSEM deal with multimapping?

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

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RSEM deal with multimapping? #206

Closed marwa38 closed 6 months ago

marwa38 commented 10 months ago

Could you please answer my below question I received from a reviewer? Include information on how the RNA-Seq aligner dealt with multimapping reads (did it output all possible alignment locations, or just a single one per read?)

Thanks M

IvonaPYF commented 7 months ago

Might be late for the original author, but if anyone has similar concerns, I would recommend reading the following review article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7330433/ especially paying attention to Table 1 and Fig. 3. You will see how different aligners work and what strategies they use.