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Minimum read length in Trimmomatic

Hello everyone,

I am using Trimmomatic to trim RNA seq data.My question is why we set the minimum read length 36? if we decrease this value, how can it effect post analysis result?

Thanks
Jan

rna-seq trimmomatic
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updated by chen chen • written by matiqau • matiqau

1 answer

You can decrease it, but too short read may cause misalignment.

And it depends on your data, if you're processing micro RNA, you should decrease it to less than 20, since micro RNA is usually 20~25 bp long.

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written by chen chen

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