sortMeRNA before or after adapters trimming ?

Question

[debitboro]

Hi Biostars community,

Shall I use sortMeRNA before or after poly(A) tails removal and/or adapters trimming ?

Thanks

Answer 1

[caggtaagtat]

If you are using it for rRNA removal, I would use it after trimming, since I basically maps the reads to the rRNA database and with trimming beforehand, the process should be improved.

However be aware, that sometimes it can happen, that a random blank line gets integraded into your data