In the beginning of my pipeline, I just fed the paired reads (2 files) into fastp, with the default options, and assumed it would do a good job preparing the reads for the next step: alignment
But I now checked the files in FastQC and it doesn't show much difference from before the fastp processing: Some extra yellow and red signals appear. I think the end result is even worse.
fastqc doesn't analyse paired reads files together. So it might be wrong regarding the paired quality, taken as a whole.
Anything else I should use together with FastQC, to verify the output quality?
I'm aligning a bunch of poolseqs and then comparing them to find consistency in the change of snp frequencies
As requested here is one of the examples that made me ask this:
Before fastp. only one problem noted by fastqc
After fastp. overall quality seems to have decreased
The raw data is a pool seq from illumina.