Question: Minimum read length in Trimmomatic
1
gravatar for matiqau
2.4 years ago by
matiqau10
matiqau10 wrote:

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 • 1.1k views
ADD COMMENTlink modified 2.4 years ago by chen2.0k • written 2.4 years ago by matiqau10
0
gravatar for chen
2.4 years ago by
chen2.0k
OpenGene
chen2.0k wrote:

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.

ADD COMMENTlink written 2.4 years ago by chen2.0k
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