Forward read data look great, paired end and reverse reads look erroneous

[robertocnava]

Hi Felix, I'm hoping you can help with an issue I'm having with paired end sequencing. I'm sequencing an amplicon that is 350bp long. The first ~300 bases on the forward read match what I expect. Biological and technical replicates match closely. When I run PE alignment, the data follows no pattern I can recognize. PE alignment is low and seemingly random. SE alignment of R2 using --pbat has an alignment rate is fine but the data doesn't make much sense to me. Would you mind taking a look? This is a repetitive region in hg38. I've also attached the unconverted amplicon.

Thank you very much for your help BISMID-NTG-200-1_S0_L001_R1_001.fastq (2).gz BISMID-NTG-200-1_S0_L001_R2_001.fastq (2).gz BISMID-NTG-200-2_S1_L001_R1_001.fastq (2).gz BISMID-NTG-200-2_S1_L001_R2_001.fastq (2).gz BIS-MID.txt

BISMID-NTG-200-3_S2_L001_R1_001.fastq (1).gz BISMID-NTG-200-3_S2_L001_R2_001.fastq (1).gz