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?
Please delete this question as it turns out to have been my misunderstanding of the datasets (2 lanes of the same end files vs paired-end files). Bismark is working great now!!