https://github.com/biomystery/ataccnv
A tool to call CNV (Copy Number Variation) from bulk ATAC-Seq data
https://github.com/biomystery/ataccnv
atac-seq bioinformatics cnv
Last synced: about 1 month ago
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A tool to call CNV (Copy Number Variation) from bulk ATAC-Seq data
- Host: GitHub
- URL: https://github.com/biomystery/ataccnv
- Owner: biomystery
- Created: 2018-06-04T22:51:40.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2018-06-04T23:29:42.000Z (about 8 years ago)
- Last Synced: 2025-03-04T15:46:25.109Z (over 1 year ago)
- Topics: atac-seq, bioinformatics, cnv
- Language: R
- Homepage:
- Size: 15.6 KB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
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README
# atacCNV
Call Copy Number Variation from ATAC-seq data.
## Useage
```Shell
export PATH=$PATH:$(pwd)
```
## List of files
* [bedToBdgBW.sh](./src/bedToBdgBw.sh): use `macs pileup` to generate pileup track (`bw`,`bdg`) from input reads (`bed`) with reads extend half of window size in both direction.
* [tagToFrag.sh](./src/tagToFrag.sh): covert `tagAlign` to fragments in `bed`, `sort.bdg` and `bw` format.
* [readsMasker.sh](./src/readsMasker.sh): filter reads (in `bed` format) by given mask regions.
* [smoothBw.sh](./src/smoothBw.sh): smooth bigwig by sliding window (size - w and step - s)
* [callCNV.R](./src/callCNV.R): call CNV from treat adjusted by mapb
## Typical Steps:
1. Get output from pipleine: `tagAlign`, `peaks` (openning regions).
2. (optional) Run [tagToFrag.sh](./src/tagToFrag.sh): get fragments `bed`, `bdg` and `bw`
3. Run [readsMasker.sh](./src/readsMasker.sh) to filter out reads or frags in peak regions and get background frags.
4. Run [smoothBw.sh](./src/smoothBw.sh) to get average coverage in each window for both control or treatment. It will reorder the bed file, so that the it cannot preserve the pair info if input is in `tagAlign` format. Please covert to fragment bed first.
5. Run [callCNV.R](callCNV.R) to get CNV regions, segment plots
## Call Wrapper:
* Input: reads (`tagAlign`), peak regions (`bed` or `narrowPeaks`), mapb track (`bw`), sliding window (`stepsize`,`windowsize`)
* Output: CNV regions (`bed`), log2CovRaito plots with segments (`pngs` and `tab`), background reads track (`bw`)