Why the Trimmomatic does not remove some adapters? How do I add a new sequence to be removed?

Question

[belenescobari]

Hello,

I am trying to trimm the adapters of my paired-end reads from a Miseq sequencing. I used the command line that is available in the manual but after "trimming" and running a second FastQC, the overrepresented sequence are still present as "Illumina Index X". I checked the "adapter" folder in the Trimmomatic and I can´t find the "Index X" that was supposed to be cut (in none of the -PE files). So my question is: How do I "add" the Index sequence to one of those files or how do I tell the Trimmomatic to clip this Index? This is the command line I used:

java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36

I have also tried the others PE.fa files.

Thanks for your replies.

[alex.zaccaron]

If you can afford use a different tool, try fastp, which can auto detect the adaptor sequence and is much faster than Trimmomatic. BBduk from BBMap is also a good one, which comes with a comprehensive list of adaptors (adapters.fa).