Genome preparation
This script needs to be run only once to prepare the genome of interest for bisulfite alignments. You need to specify a directory containing the genome you want to align your reads against (please be aware that the bismark_genome_preparation script expects FastA files in this folder (with either .fa or .fasta extension, single or multiple sequence entries per file). Bismark will create two individual folders within this directory, one for a C->T converted genome and the other one for the G->A converted genome. After creating C->T and G->A versions of the genome they will be indexed in parallel using the indexer bowtie2-build (or hisat2-build). Once both C->T and G->A genome indices have been created you do not need to use the genome preparation script again (unless you want to align against a different genome...).
Again, please note that Bowtie 2 and HISAT2 indexes are not compatible! To create a genome index for use with HISAT2 the option --hisat2 needs to be included as well.
Running bismark_genome_preparation
USAGE: bismark_genome_preparation [options] <path_to_genome_folder>
A typical command could look like this: