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https://github.com/alexpreynolds/freq-counter

Count letter frequencies in sliding windows over a genome
https://github.com/alexpreynolds/freq-counter

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Count letter frequencies in sliding windows over a genome

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# 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`.