MethPipe

MethPipe: a computational pipeline for analyzing bisulfite sequencing data

The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS).

Quick start

Tools

Program Description
rmapbs, rmapbs-pe map bisulfite treated short reads
duplicate-remover remove duplicate reads
methcounts calculate methylation level and read coverage at individual sites
bsrate estimate bisulfite conversion rate
hmr identify hypo-methylated regions
hypermr identify hyper-methylation in plants and organisms showing mosaic methylation
pmd identify large partially methylated domains
amrfinder identify allele-specific methylated regions
roimethstat compute methylation level by genomic region of interest
mlml consistently estimate 5-mC and 5-hmC levels. See MLML homepage.
Table 1: List of tools in the MethPipe package

Workflow

Workflow for analyzing bisulfite sequencing data (WGBS)

Figure 1: Work flow of the MethPipe package for analyzing bisulfite sequencing dataset

Contact

Please send emails to the methpipe mailing list at
methpipe@googlegroups.com if you have any questions,
suggestions or comments.

To join the mailing list, send an email to methpipe+subscribe@googlegroups.com

View previous messages at MethPipe and MethBase Users’ Mailing List

References

Song Q, Decato B, Hong E, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD (2013) A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLOS ONE 8(12): e81148 [PDF] [Publisher Site]