fa-gc¶
Use fa-gc to calculate the GC content surrounding a given genomic position.
The window sizes correspond to the distance upstream and downstream used to calculate GC content for. For example:
- 50 –> “100bp” window, but a 101bp width is examined.
Example output:
> sc fa-gc --pos pos.tsv hg19.fa.gz 50 3200 500000
| chrom | pos | gc_100 | gc_6400 | gc_1000000 |
|---|---|---|---|---|
| chr1 | 50000 | 0.3663 | 0.373535 | 0.430292 |
| chr1 | 50020 | 0.3663 | 0.373535 | 0.430288 |
| chr1 | 50050 | 0.3564 | 0.373067 | 0.430283 |
Notes
- GC content calculations omit
Nbases. - Output is sorted by chromosome, position.