Difference between revisions of "Methpipe"
| (6 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
{{Bioinformatics application | {{Bioinformatics application | ||
|sw 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). | |sw 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). | ||
| − | |bio domain= | + | |bio domain=Epigenetics, DNA methylation, Sequencing, |
| − | |bio method=Bisulfite mapping | + | |bio method=Bisulfite mapping, |
| − | |bio tech=Illumina, | + | |bio tech=Illumina, Illumina HiSeq, Illumina Solexa, |
|created by=Song Q et al | |created by=Song Q et al | ||
|created at=University of Southern California, | |created at=University of Southern California, | ||
| Line 15: | Line 15: | ||
== Description == | == Description == | ||
<!-- Describe the application in the space below --> | <!-- 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 | ||
| + | |} | ||
Latest revision as of 19:08, 19 December 2015
|
Application data |
|
| Created by | Song Q et al |
|---|---|
| Biological application domain(s) | Epigenetics, DNA methylation, Sequencing |
| Principal bioinformatics method(s) | Bisulfite mapping |
| Technology | Illumina, Illumina HiSeq, Illumina Solexa |
| 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).
"Error: no local variable "counter" was set." is not a number.
Description
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 |
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 |
|---|---|---|
