Closed wangyugui closed 7 years ago
@wangyugui , in that case, you could just add rRNA in your reference. Then if you do not want rRNAs, you could remove them from RSEM result files and renormalize the expression of rest isoforms to be 10^6.
Hope it helps, Bo
Is there a tool to renormalize the expression of rest isoforms?
@wangyugui , no. But it is very simple, you can write a script yourself: summing all TPMs for transcripts of interest and then making this sum into 10^6.
Thanks a lot for your answer.
Is it posssible to mask/ignore rRNA when rsem-calculate-expression, but not rsem-prepare-reference.
If we add rRNA to ref, we can get the rRNA rate from the result bam file , and Less false positive when mapping.