We did WGBS for our fish samples and I am currently trimming our raw reads using the fastp (Version 0.20.0) and TrimGalore! (Version 0.6.10) software. however, when I did quality checking of the trimmed sequences using FastQC (version 0.12.1) I noticed that my reads both in raw sequences and trimmed sequences (trimmed using fastp and TrimGalore!), specifically on [filename]_2 sequences (reverse sequences), have a high poly-A content. I already included the "--trim_poly_x" in fastp but it did not do any significant decrease when I did FastQC.
Edit: I attached the fastqc report, specifically for the reverse sequences, for the before (first picture) and after (second picture) trimming.
I hope someone could enlighten me regarding this