Difference between revisions of "Methpipe"
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| + | {| class="wikitable" | ||
| + | |+ List of tools in MethPipe | ||
| + | |- | ||
| + | ! 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 | ||
| + | |} | ||
Revision as of 09:25, 12 September 2013
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Application data |
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| Created by | Song Q et al |
|---|---|
| Biological application domain(s) | Epigenomics, DNA methylation, Bisulfite Sequencing |
| Principal bioinformatics method(s) | Bisulfite mapping, Analysis Pipeline |
| Technology | Illumina |
| Created at | University of Southern California |
| Maintained? | Yes |
| Input format(s) | FASTQ, SAM/BAM |
| Programming language(s) | C++ |
| Licence | GPL (>= 3) |
| Operating system(s) | Linux, Mac OS X |
| Contact: | methpipe@googlegroups.com |
Summary: 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).
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Description
| 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 |
Links
- Methpipe Homepage [ edit link ]
- Methpipe Mailing list [ edit link ]
- Methpipe Manual [ edit link ]
- Methpipe Related [ edit link ]
- Methpipe Related [ edit link ]
- Methpipe Source code [ edit link ]
References
To add a reference for Methpipe, enter the PubMed ID in the field below and click 'Add'.
[ edit box ]
Search for "Methpipe" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
