Ran Bismark using our high performance computing (HPC) node, Mox, with two different bowtie2 settings:
The second setting is a bit less stringent than the default settings and should result in a higher percentage of reads mapping. However, not entirely sure what the actual implications will be (if any) for interpreting the resulting data.
Input data was previously trimmed per Bismark’s recommendation for Illumina TruSeq libraries (TrimGalore! 5’ 10bp):
List of input files and Bismark configurations can be seen in the SLURM scripts: