I'm using Bismark for the first time, and 99.99% of the reads are failing to align for my paired dataset of seq length 51 bp. I have tried using the default
-l, as well as
-l of 40, the default
-n as well as
-n of 1, the original fastq files as well as quality trimmed and adaptor cut ones, etc., but none of these variations have made much of a difference. The FastQC output shows that the per base and per sequence quality scores are very good. Do you have any suggestions on how to proceed?