I'm new to bisulfite sequencing. Recently received my paired-end WGBS raw file. The Read1 looks OK after fastQC, but the Read2 file has a waired 'Per base sequence content' figure. Why is there a such G content. It is supposed to be very low G reading due to C-T conversion in Read1 file.
The Q value of each file is high (>30). They all passed fastQC adapter content test.
What could cause this problem? Is it wise to trim the 1-15bp in Read2?