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https://github.com/cmdcolin/jbrowse-plugin-riboseq
A WIP for a biostar question
https://github.com/cmdcolin/jbrowse-plugin-riboseq
Last synced: 4 days ago
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A WIP for a biostar question
- Host: GitHub
- URL: https://github.com/cmdcolin/jbrowse-plugin-riboseq
- Owner: cmdcolin
- Created: 2024-04-01T16:45:10.000Z (8 months ago)
- Default Branch: master
- Last Pushed: 2024-04-01T17:10:58.000Z (8 months ago)
- Last Synced: 2024-04-15T02:14:35.478Z (7 months ago)
- Language: TypeScript
- Size: 225 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# jbrowse-plugin-ribo-seq
## Dev setup
```bash
git clone [email protected]:cmdcolin/jbrowse-plugin-ribo-seq
cd jbrowse-plugin-ribo-seq
yarn
yarn start
# visit http://yourjbrowse/?config=http://localhost:9000/config.json
```
## Production setup
```json
{
"plugins": [
{
"name": "RiboSeq",
"url": "https://unpkg.com/jbrowse-plugin-ribo-seq/dist/jbrowse-plugin-ribo-seq.umd.production.min.js"
}
]
}
```
## Screenshot
## Input
sample data: a bed tabix file with a column name indicating "color"
```
#chr start end strand color count
1 10000000 10000001 + 0 6
1 10000001 10000002 + 0 1
1 10000004 10000005 + 1 1
1 10000006 10000007 + 2 1
1 10000007 10000008 + 1 30
1 10000009 10000010 + 3 2
```
## Configuration
Use the RiboSeqAdapter and then use a BedTabixAdapter subadapter
```json
{
"type": "FeatureTrack",
"trackId": "ribo-seq_track",
"name": "RiboSeq",
"assemblyNames": ["hg19"],
"adapter": {
"type": "RiboSeqAdapter",
"subadapter": {
"type": "BedTabixAdapter",
"scoreColumn": "count",
"bedGzLocation": {
"uri": "test.bed.gz"
},
"index": {
"location": {
"uri": "test.bed.gz.tbi"
}
}
}
},
"displays": [
{
"displayId": "ribo-seq_display",
"type": "LinearRiboSeqDisplay"
}
]
}
```
## Footnote
Motivated by https://www.biostars.org/p/9591324/#9591469
This is very demo-quality. Inspired by plugins like
https://github.com/cmdcolin/mpileupplugin also