I have 8 samples and paired-end
methyl-seq data for all of them. I have a serious problem with alignment of these files. when I aligned as paired-end (R1 and R2 together), the alignment rate is 4-5 % but if I align each file separately (R1 and R2 separately), the alignment rate would be at least 70 %. I have checked everything including the reference file to make sure there is no mistake. I also tried different aligners and different parameters but got similar results. for sure, the problem happened in the lab when processing the samples or during the sequencing. I have no idea in which step the problem happened. do you have any idea what could be the problem?