Can rnaspades be used to treat metatranscriptomic data?

[Holly202109]

Is your feature request related to a problem? Please describe.

HI, thanks for the great tool. I am interested in rnaspades, I would like to know whether rnaspades can be used to treat metatranscriptomic data. Thank you.

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[asl]

@Holly202109 Please do not create issues for the generic questions as you were advised. Tagging @andrewprzh

[andrewprzh]

Hi!

We have tested rnaSPAdes on metatranscriptomic data, but not a lot. I'd say it gives better results that metaSPAdes or usual SPAdes, and it's definitely safe to run it. You may expect a bit of redundancy in the resulting contigs since rnaSPAdes tries to reconstruct alternative isoforms typical for eukaryotic genomes.

Best
Andrey

[Holly202109]

Thanks a lot, Andrey. I got it and will use it to assemble my metatranscriptomic reads. Do you think I should remove the rRNA reads before the assembly step? or should include them? Best regards Liping

…

-----原始邮件----- 发件人:"Andrey Prjibelski" ***@***.***> 发送时间:2021-06-25 19:25:34 (星期五) 收件人: ablab/spades ***@***.***> 抄送: Holly202109 ***@***.***>, Mention ***@***.***> 主题: Re: [ablab/spades] Can rnaspades be used to treat metatranscriptomic data? (#799) Hi! We have tested rnaSPAdes on metatranscriptomic data, but not a lot. I'd say it gives better results that metaSPAdes or usual SPAdes, and it's definitely safe to run it. You may expect a bit of redundancy in the resulting contigs since rnaSPAdes tries to reconstruct alternative isoforms typical for eukaryotic genomes. Best Andrey — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[andrewprzh]

You may try removing rRNA either from reads or from contigs, my guess is that the results will be quite similar. You may try both strategies if you have time :)
Unfortunately, I cannot say for sure which one is better.