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genomica 03-21-2016 06:47 AM

rRNA removal for RNAseq analysis
Hi all,

Do you think we need to filter rRNA and low complexity reads from Poly-A selected total mRNAseq stranded data before performing RNAseq analysis (tophat2-htseq-deseq2)? I am sorry if I have missed any previous post on similar matter.

Thanks for your help.

fanli 03-21-2016 01:31 PM

Generally not necessary, but it doesn't really hurt. Also, depending on what GTF file you provide to htseq, rRNAs may be excluded anyways.

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