Minimum read length in Trimmomatic

Question

[matiqau]

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

Answer 1

[chen]

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.