https://github.com/epigen/biseqmethcalling
Methylation calling script for bisulfite sequencing
https://github.com/epigen/biseqmethcalling
Last synced: 10 months ago
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Methylation calling script for bisulfite sequencing
- Host: GitHub
- URL: https://github.com/epigen/biseqmethcalling
- Owner: epigen
- Created: 2016-12-08T08:03:32.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2016-12-08T08:39:33.000Z (over 9 years ago)
- Last Synced: 2023-10-20T19:42:16.139Z (over 2 years ago)
- Language: Python
- Homepage:
- Size: 70.3 KB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# biseqMethCalling
* __Title:__ biseqMethCalling
* __Description:__ Methylation calling script for bisulfite sequencing
* __Authors:__ Christoph Bock, Natalie Jaeger, Fabian Mueller, Michael Ziller
* __Version:__ 2012-08-22
The following methods are supported
* Whole genome bisulfite sequencing (WGBS)
* Reduced-representation bisulfite sequencing (RRBS)
* Hybrid-selection bisulfite sequencing
* Other variants of region-specific bisulfite sequencing (e.g. MethylCap-biseq and ChIP-biseq)
By default CpGs are analyzed, but other sequence contexts (CpA, CpH, CpHpG, etc.) are also supported.
## Usage
The main script is `biseqMethCalling.py`. See `python biseqMethCalling.py --help` for a full listing of parameters
### Input
* (multiple) BAM files containing containing read alignments
* parameters (see --help for more info)
### Output
* statistics (see code documentation for details)
* CpGs with genomic coordinates and methylation ratios as a bed file
* Fragment coverage: coordinates, readcounts and CpG methylation ratios of each generated fragment (RRBS: MspI digestion, WGBSS: Paired end reads)
* Reads: coords (read and fragment the read is on), CpG (possibly other patterns) of __processed__ reads
* ReadDetails: more detailed read info for processed reads including base quality details, alignment/mismatch details, conversion rates, ...
* runtime profile files for each processed region, if desired
* if the verbose option is set: information on the processed windows/regions
* log files
* a vast amount of temporary files for each processed region
## Note
This is an archiving repository and the contained code is currently not actively maintained.