# htseq-count

**Galaxy Tool ID**: `toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1+galaxy1`
**Version**: 0.9.1+galaxy1
**Category**: RNA-seq

> - Count aligned reads in a BAM file that overlap features in a GFF file

## Example Query

> "Run htseq-count on my data"

## Run via Galaxy Bridge

```bash
python galaxy_bridge.py --tool-details toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1+galaxy1
python galaxy_bridge.py --run toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1+galaxy1 --input <file> --output <dir>
```

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*Auto-generated from usegalaxy.org tool index*
