I have been using Galaxy's Trim galore for clipping adapters from Illumina small RNA sequences. While using automatic adapter detection, I noticed that the adapter being removed is 'ATGGAATTCTCG'. However, in Trim galore's change log from 2015 it is mentioned:
12-11-15: Version 0.4.1 released: Essential update for smallRNA libraries!
Changed the Illumina small RNA sequence used for auto-detection to 'TGGAATTCTCGG' (from formerly 'ATGGAATTCTCG'). The reason for this is that smallRNA libraries have ssRNA adapters ligated to their -OH end, a signature of dicer cleavage, so there is no A-tailing involved.
Can this be please corrected? Meanwhile, is it fine if we perform 'user defined adapter trimming' by providing the sequence 'TGGAATTCTCGG' manually?
Thank you. PG