(I) Running bismark_genome_preparation USAGE:bismark_genome_preparation [options] <path_to_genome_folder>

A typical genome indexing could look like this:

--

(II) Running bismark

USAGE: bismark [options] <genome_folder> {-1 <mates1> -2 <mates2> |

<singles>}

Typical alignment example (tolerating one non-bisulfite mismatch per read):

bismark -n 1 -l 50 /data/genomes/homo_sapiens/GRCh37/ test_dataset.fastq

February 06, 2012

This will produce two output files:

(a) test_dataset.fastq_bismark.sam (contains all alignments plus methylation call strings)

(b) test_dataset.fastq_bismark_mapping_report.txt (contains alignment and methylation summary)