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update README
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stevekm committed Nov 11, 2020
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Expand Up @@ -36,19 +36,12 @@ $ python make_IGV_snapshots.py test_data/test_alignments.bam test_data/test_alig

See `python make_IGV_snapshots.py --help` for available options. Here are a few:

- `-r`: Path to the BED formatted regions file to use:
```bash
$ python make_IGV_snapshots.py /path/to/alignments1.bam /path/to/alignments2.bam -r /path/to/my_peaks.bed
```

- `-nosnap`: Make batchscript without taking snapshots:
```bash
$ python make_IGV_snapshots.py /path/to/alignments1.bam /path/to/alignments2.bam -nosnap
```
- `-r`: Path to the BED formatted regions file to use (defaults to the included demo `regions.bed`)
- `-nosnap`: Make batchscript without taking snapshots
- `-g`: Genome to use, e.g. `hg19`
- `-ht`: Height of the snapshot, default is 500
- `-o`: Name of the output directory to save the snapshots in.
- `-bin`: Path to the IGV jar binary to run
- `-o`: Name of the output directory to save the snapshots in (defaults to `IGV_Snapshots`)
- `-bin`: Path to the IGV jar binary to run (defaults to `igv.jar`)
- `-mem`: Memory to allocate to IGV (MB)
- `-suffix`: Filename suffix to place before '.png' in the snapshots
- `-onlysnap`: Skip batchscript creation and only run IGV using the supplied batchscript file
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