Hi,
I am new to RNASeq analysis and have some sequences aligned by STAR.
I am planning to use HTSeq count to generate an input file for DeSeq, but learned now that HtSeq will discard multi-mappers. Is there a way to make it accept multimappers? Or is there another program like easyRNASeq that does not discard multimappers? I do have 10-35% multimappers in my data set.
Thanks!
I am new to RNASeq analysis and have some sequences aligned by STAR.
I am planning to use HTSeq count to generate an input file for DeSeq, but learned now that HtSeq will discard multi-mappers. Is there a way to make it accept multimappers? Or is there another program like easyRNASeq that does not discard multimappers? I do have 10-35% multimappers in my data set.
Thanks!
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