Prepare Reference Files
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The reference files required for making the MappingConfig file is listed below
I download reference FASTA from the . For mapping, I will keep all the small contigs to make sure all reads mapped properly, but I usually remove them and only focus on the main chromosomes for further analysis.
Another thing is the lambda DNA spike-in as a non-conversion estimation (we do that), I usually append the with the name chrL to my genome FASTA. You can download the chrL from and append that to your genome.
Use bismark to prepare the genome index, see its documentation . Note that we use bowtie2 for snmC-seq and snmCT-seq (that's bismark's default also), and bowtie1 for snm3C-seq ().
For human and mouse, we usually use . But I do not update GTF throughout the same project. (And the difference between versions probably have little impact on your analysis results.)
Use STAR to prepare its genome index, see its documentation .