remove rrna from rna seq

Question

[yueli7]

Hello,

Human RNA-seq data, after remove adaptor and primer, do I need to remove rRNA?

Thanks in advance for great help!

Yue Li

[yueli7]

Devon Ryan,

Thank you so much for your great help!

Yue

[WouterDeCoster]

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Answer 1

[Devon Ryan]

As a rule of thumb, no you don't you also don't generally need to remove adapters, since programs like STAR will perform local alignment anyway. This assumes you're not trying to assemble the transcriptome or something like that though.

[JJ]

So it's always required for transcriptome assembly though? Would you recommend it when using HISAT2 and Stringtie with a known (and good) annotation but with the goal of discovering new transcripts / isoforms?

[Devon Ryan]

It's only needed for de novo assembly, which doesn't apply to StringTie. However, since HISAT2 (unlike STAR) can't perform local alignment you'll probably need to trim your reads for it to produce acceptable results. Alternatively, drop HISAT2 and move to STAR.

[JJ]

Thank you! Do STAR and Stringtie work well together? Is there anything to watch out for? What I really like about HISAT2 is that it's very fast (I have a lot of samples) and it can work directly from the SRA repository.

[Devon Ryan]

STAR is faster than HISAT2 and works just fine with stringTie.