https://github.com/keller-mark/vitessce-demo-sc-atac-seq-10x-genomics
Data processing for a demo of vitessce + higlass
https://github.com/keller-mark/vitessce-demo-sc-atac-seq-10x-genomics
Last synced: 3 months ago
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Data processing for a demo of vitessce + higlass
- Host: GitHub
- URL: https://github.com/keller-mark/vitessce-demo-sc-atac-seq-10x-genomics
- Owner: keller-mark
- Created: 2020-03-02T21:03:46.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-08-08T21:05:40.000Z (almost 5 years ago)
- Last Synced: 2025-01-12T14:10:58.624Z (5 months ago)
- Language: Python
- Size: 15.6 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
Vitessce branch: [`keller-mark/sc-atac-demo-v2`](https://github.com/hubmapconsortium/vitessce/tree/keller-mark/sc-atac-demo-v2)
Demo: http://s3.amazonaws.com/vitessce-data/demos/2020-06-22/24f33f0/index.html?dataset=sc-atac-10x-pbmc&theme=light
Set up and activate conda environment:
```sh
conda env create -f environment.yml
conda activate vitessce-demo-sc-atac-seq-10x-genomics
```
Run snakemake:
```sh
snakemake --cores 1
```
Ingest the tilesets for all 10 clusters, using [higlass-server](https://github.com/higlass/higlass-server).
The script takes as an argument the relative path to the higlass server directory.
```sh
bash run_ingest.sh ../../higlass/higlass-server
```
Note: the above command may generate the following warnings `tilesets.models.DoesNotExist: Tileset matching query does not exist.`