Pao-Yang Chen, Shawn Cokus, and Matteo Pellegrini
Department of Molecular, Cell and Developmental Biology, 
University of California, Los Angeles http://pellegrini.mcdb.ucla.edu/Lab/Home.htmlshapeimage_2_link_0
Download BS Seeker BS_SEEKER.tgzBS_Seeker_files/BS_SEEKER.tgzshapeimage_4_link_0
Supplementary Information (BSS_Supp.pdf)BS_Seeker_files/BSS_Supp.pdfshapeimage_5_link_0
Examples for running BS SeekerEXAMPLES.htmlEXAMPLES.htmlshapeimage_6_link_0

Type “ tar -xzvf BS_SEEKER.tgz ” to extract the files

Bowtie is required for running BS Seeker
Download Bowtie alignerhttp://bowtie-bio.sourceforge.net/index.shtmlhttp://bowtie-bio.sourceforge.net/index.shtmlhttp://bowtie-bio.sourceforge.net/index.shtmlshapeimage_7_link_0shapeimage_7_link_1
UsageUSAGE.htmlshapeimage_8_link_0

BS Seeker performs accurate and fast mapping of bisulfite-treated short reads. It aligns Bisulfite-treated reads generated from the Cokus et al's library protocol (with tags) or the Lister et al's library protocol (with no tags), see Fig_1_Prepare_Libaraies.pdf.