As you can see here, I have done Fastqc on my fastq. The reads have a 125 nucleotides length.
There is no overrepresented sequence even if I can see there are Universal TrueSeq Adaptators at the end . 1- Is this insignificant ? Do you think I need to remove them ?
I'd like to try to remove this adaptators using Trimmomatic or (fastqX toolkit or cutadapt) I don't want to be too stringent specifying a given length..First I really want to remove this specific adaptator at the end of my read.
2- By the way, what is the accepted cutoff by community for filtering by quality, Qqual 30 or less ? Given the quality picture above, what kind of threshold would you use ? using Qqual or ReadLength ? Personnaly, I was thinking to use Qual 20 or 115 for readLength/
In trimmomatic you can remove ILLUMINACLIP:TruSeq3-PE or ILLUMINACLIP:TruSeq2-PE depending on the library used. You can configure yourself a file with your adaptors. I read stuffs here and here about Illumina adaptators but i'm not sure about the sequence to use.
So does someone has already remove Universal TrueSeq Adaptators in Trimmomatic ? What would you use as sequence Adaptator ? and is this really necessary to remove this adaptators knowing that an Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis