Question: remove rrna from rna seq
0
gravatar for yueli7
5 months ago by
yueli740
China
yueli740 wrote:

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 • 291 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by yueli740

Devon Ryan,

Thank you so much for your great help!

Yue

ADD REPLYlink written 5 months ago by yueli740

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

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ADD REPLYlink written 5 months ago by WouterDeCoster32k
4
gravatar for Devon Ryan
5 months ago by
Devon Ryan85k
Freiburg, Germany
Devon Ryan85k wrote:

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.

ADD COMMENTlink written 5 months ago by Devon Ryan85k

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?

ADD REPLYlink written 5 months ago by JJ350
2

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.

ADD REPLYlink written 5 months ago by Devon Ryan85k

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by JJ350
2

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

ADD REPLYlink written 5 months ago by Devon Ryan85k
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