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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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mask/ignore rRNA when rsem-calculate-expression, but not rsem-prepare-reference #53

Closed wangyugui closed 7 years ago

wangyugui commented 7 years ago

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.

bli25wisc commented 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

wangyugui commented 7 years ago

Is there a tool to renormalize the expression of rest isoforms?

bli25wisc commented 7 years ago

@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.

wangyugui commented 7 years ago

Thanks a lot for your answer.