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  • genomica
    Junior Member
    • Feb 2013
    • 9
    #1

    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.
    Tags: None
    • fanli
      Senior Member
      • Jul 2014
      • 197
      #2
      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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