I have 8 samples and
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.
do you know what could be the problem? is there any way to check what the problem is?