I performed trimmomatic in order to remove adapter sequences (trueseq3, Illumina).
First I have used truseq3-PE.fa file as adapters and observed still few adapters in sequences.
Then, I have used trueseq3-PE-2.fa file which has reverse complements too. It removes all adapters. Can I assume that this file will be used by default?
In addition it removed some of my reads (Out of 22Million, 4Million reds were removed). When I used 2:30:10:8:TRUE it kept reads without removing.
I read article but got little confused. In article it was mentioned that removed sequences are not useful sequences and formed by ligation of adapters.
Is it safe to remove sequences by using default 2:30:10 or should I keep using 2:30:10:8:TRUE?
Could you please help me to understand this bit clear.
Thanks In Advance