TrimGalore! not properly removing low quality base calls.
Hello all,
I've recently been attempting to trim a set of scRNA-Seq fastqs for alignment and analysis which show fairly poor quality using TrimGalore with the following parameters:
~/TrimGalore-0.6.6/trim_galore --path_to_cutadapt ~/.local/bin/cutadapt --illumina --paired --phred33 -q 20 -j 8 -o outdir R_1.fq.gz R_2.fq.gz
This successfully removes adapters, but does not appear to remove low quality base calls (<20Q) as I'd expect. I had used TrimGalore some time ago and didn't have this problem.
Help or explanation would be appreciated! Maybe I'm misinterpreting something.
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You can find the explanation here: https://cutadapt.readthedocs.io/en/stable/algorithms.html#quality-trimming-algorithm
Assuming your screenshot is based on trimmed data you can see that the quality around the 150 is higher than lets say position 120. I guess the quality of position 150 is high enough to make the trimming algorithm stop.