sept 1. Bismark预处理

./bismark_genome_preparation --path_to_bowtie /home/bowtie --verbose --bowtie2 /home/chromFa.mm9

sept 2. bismark比对

./bismark /home/chromFa.mm9 --path_to_bowtie /home/bowtie --bowtie2 -1 /home/targetR1.fq -2 /home/targetR2.fq -o /home

sept 3. Bismark methylation extractor

./bismark_methylation_extractor -p --no_overlap –report target.sam -o /bismark

=============================

附录1：Bismark项目主页

http://www.bioinformatics.babraham.ac.uk/projects/bismark/

How to use Bismark