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Short description:
Please summarise the application in a few sentences. Avoid links here. The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools for identifying higher-level methylation features, such as hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR).
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Epigenetics, DNA methylation, Sequencing,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Bisulfite mapping,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina, Illumina HiSeq, Illumina Solexa,
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
University of Southern California,
== Description == <!-- Describe the application in the space below --> === List of tools in MethPipe === {| class="wikitable" |- ! 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 |- |hmr_plant || identify hyper-methylation in plants and organisms showing mosaic methylation |- |pmd || identify large partially methylated domains |- |amrfinder || identify allele-specific methylated regions |} <!-- -->
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