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
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附录1：Bismark项目主页
http://www.bioinformatics.babraham.ac.uk/projects/bismark/
原文：http://www.cnblogs.com/lyhonk/p/3931773.html