low alignment rate of methyl-seq data

Question

[Sara]

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?

[ATpoint]

You would need some details. Which tools, which command lines. Organism etc.

[Sara]

@ATpoint: I used bismark and data is from Pork. bismark --quiet --bowtie2 --multicore 12 -n 1 /bismark_aln/genomes/ -1 bone.lane7.R1_val_1.fq.gz -2 bone.lane7.R2_val_2.fq.gz