Trimmomatic adapters removal

Question

[vrehaman]

Dear Team,

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

Fazulur Rehaman

Answer 1

[Devon Ryan]

I would generally set keepBothReads to TRUE, so 2:30:10:8:TRUE would seem better, since you then have both pairs. Granted, you'll have more pairs that completely overlap, but few aligners have issues with that any more.

[vrehaman]

Hi Devon,

Thanks a lot for your response.

Yeah I am also using the same option. And still I am not clear why they are not useful sequences which were removed using palindrome mode of Trimmomatic. Any comments on this.

Thanks & Regards Fazulur Rehaman