Trimmomatic only for removing adapters

Question

[grant.hovhannisyan]

Hi Biostars,

I need to cut only adapters from my data using trimmomatic. I used the following command:

 java -jar /home/ghovhannisyan/Softs/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 11 read1.fastq read2.fastq read_1P.fastq read_1U.fastq read2.fastq read_2P.fastq read_2U.fastq \
ILLUMINACLIP:adapters/TruSeq3-PE-2.fa:2:30:10 MINLEN:50

The question is - with the command above, will trimmomaitc remove only adapters and reads less than 50 bp? Because from the result that I get it seems like it also removes reads based on quality scores, which I don't want. Are there any default values for cutting options even if you don't specify them?

thanks

[jenn.drummond]

I'm having a similar experience -- is it possible to get Trimmomatic not to eliminate reads that match adapter, and just trim them off instead? My parameters are

java -jar trimmomatic-0.32.jar PE -threads 1 -phred33 -trimlog /dev/null \
    [input and output files] \
    ILLUMINACLIP:[adapter file]:3:30:1:1:TRUE

I've got 2x300bp reads, and I'm perfectly happy to let my downstream pipeline handle issues of length and quality. Most of the reads that are being eliminated are "Reverse Only Surviving". I understand from this post that design intent is to drop the reverse reads when a forward read is trimmed; but what if the reverse read turns out to be the useful one? I just want Trimmomatic to remove the bases that it thinks belong to adapter sequences, and leave the rest alone for further processing elsewhere.

Apologies if this should be a separate question, but I think it's in line with what the OP really wants to know, which is why reads are being eliminated and how to stop it from happening. The conjecture that it's stealth quality filtering is really just a red herring.

[lieven.sterck]

not sure about Trommomatic, but other tools can do this indeed, eg. BBduk (from the top of my head)

[ATpoint]

Cutadapt, Skewer, BBduk, just to name a few.

Answer 1

[h.mon]

The above command will trim only adapters and remove reads shorter than 50bp. Why do you think Trimmomatic is performing quality trimming?

[ATpoint]

OP probably thinks that because some trimmers have defaults for trimming trailing bases if below a certain base quality. From what I understand from the manual, Trimmomatic has no such presettings (still I typically trim for a trailing base quality above 30).

[grant.hovhannisyan]

Thanks. I thought it removes reads even without specifying the trimming parameters because I have processed a file containing ca 5 % of adapters, and the trimmomatic has removed around 10 % of reads.