Thank you, the adapter sequences are specified as CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA is the SampleSheet.csv file from the sequencing run. So I ran cut adapt on a single sample:
cutadapt \
-a CTGTCTCTTATACACATCT -A ATGTGTATAAGAGACA \
--cores 4 \
-o {output.r1} -p {output.r2} \
{input.r1} {input.r2}
The resulting log file claims:
Total read pairs processed: 68,426,019
Read 1 with adapter: 1,034,464 (1.5%)
Read 2 with adapter: 1,216,834 (1.8%)
But I see little impact on the before:
to after fastqc:
Are there other sequences I should be trimming? The kit is Illumina DNA RNA UDI SetA T agmentation DNA PCRFree so I am not sure if there would be primer dimer sequences to remove based on it being a PCR free kit unless I am misunderstanding (I am new)
I would trim it. Two percent is not much but with WGS, say you have 400mio reads per sample or so, it's still millions of reads that theoretically could contaminate variant calls. Do it once, properly, and never care about it again. That having said, we are utterly flattered with a free-to-use powerful HPC at our university, so all we do is waiting for this job to complete. If you're on a bidget, say need to pay for HPC or a cloud service, you might want to skip it, but I would still feel safer trimming.