```
infer_eperiment.py --help
```

Usage: infer_experiment.py [options]


Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -i INPUT_FILE, --input-file=INPUT_FILE
                        Input alignment file in SAM or BAM format
  -r REFGENE_BED, --refgene=REFGENE_BED
                        Reference gene model in bed fomat.
  -s SAMPLE_SIZE, --sample-size=SAMPLE_SIZE
                        Number of reads sampled from SAM/BAM file.
                        default=200000
  -q MAP_QUAL, --mapq=MAP_QUAL
                        Minimum mapping quality (phred scaled) for an
                        alignment to be considered as "uniquely mapped".
                        default=30