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