https://github.com/edawson/genelist_to_bed
Convert a list of genes to a bedfile
https://github.com/edawson/genelist_to_bed
Last synced: 4 months ago
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Convert a list of genes to a bedfile
- Host: GitHub
- URL: https://github.com/edawson/genelist_to_bed
- Owner: edawson
- Created: 2017-09-11T14:25:57.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2017-10-16T18:41:43.000Z (over 7 years ago)
- Last Synced: 2025-01-07T20:47:10.016Z (5 months ago)
- Language: Shell
- Size: 9.77 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
genelist_to_bed : make a bed file for a list of genes
-------------
Eric Dawson
September 2017
## Requirements:
Python 2.7
pyensembl (Hammer lab)
## Setup
1. Install pyensembl
`pip install pyensembl`
2. Cache ensembl DB release for genome of choice (HG19: version 75, HG38: 76-90 or newer)
`pyensembl install --release 75 --species homo_sapiens`
This will take several minutes and will download >3GB of data.
## Usage:
`python genelist_to_bed.py `
## Advanced function
## License:
MIT