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remove rrna from rna seq

Hello,

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

Thanks in advance for great help!

Yue Li

rna-seq
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written by yueli7 yueli7

Devon Ryan,

Thank you so much for your great help!

Yue

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written by yueli7 yueli7

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written by WouterDeCoster WouterDeCoster

1 answer

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.

• 1 views • link
written by Devon Ryan Devon Ryan

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?

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written by JJ JJ

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.

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written by Devon Ryan Devon Ryan

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.

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written by JJ JJ

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

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written by Devon Ryan Devon Ryan

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