https://github.com/alexpreynolds/freq-counter
Count letter frequencies in sliding windows over a genome
https://github.com/alexpreynolds/freq-counter
Last synced: 26 days ago
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Count letter frequencies in sliding windows over a genome
- Host: GitHub
- URL: https://github.com/alexpreynolds/freq-counter
- Owner: alexpreynolds
- Created: 2019-03-11T21:13:21.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-03-12T08:11:48.000Z (about 6 years ago)
- Last Synced: 2025-02-17T16:39:50.506Z (4 months ago)
- Language: C++
- Size: 25.4 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# freq-counter
We slide windows over a FASTA file and count how many of one or more characters appear in the window.
Standard output is written in BED format.
## Example
```
$ ./freq-counter --chars="AG" --span=20 --step=1 ../data/GRCh38_no_alts.fa | starch --omit-signature - > ../results/GRCh38_no_alts.counts_AG.starch
```
Replace `AG` with other character sets (`CT` etc.).
The resulting file is very large, so we compress it here with [BEDOPS](https://github.com/bedops/bedops) `starch`.