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multiple mapping using tophat2

Hi,

I want to include the gene paralogs by using tophat2 "non-uniquely mapping" to allow multiple reads aligned to the reference genome. I used default -k =1, and -m = int, will this make non-uniquely mapping achieved?

First time doing the mapping, thanks a lot for the help!

Best,
Ellie

rna-seq
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updated by Ram Ram • written by Jingyue • Jingyue

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