Commit b080cfda authored by Beatrice Tan's avatar Beatrice Tan

Update README.md

parent 2b030fc3
......@@ -21,7 +21,7 @@ cd CNAprioritization
- Set workdir to the directory where the output should be saved.
- Set gisticdir to the directory where GISTIC2 should be installed or where GISTIC2 has already been installed.
5. Specify which input dataset to use or download. There are three options for input data:
5. Specify which input dataset to use or download in config.yaml. There are three options for input data:
- Use your own dataset as input by specifying "input_file".
- Leave all settings as default to use a test dataset on Skin Cutaneous Melanoma (SKCM) tumor samples.
- Download Firehose data for a tumor type of interest:
......@@ -30,7 +30,7 @@ cd CNAprioritization
- Set date_data to the date of interest to specify which version of the dataset to use, e.g. "2016_07_15"
- See http://gdac.broadinstitute.org/runs/info/analyses__runs_list.html for older versions.
6. The settings for running GISTIC2.0 and for benchmarking can be modified if necessary (see Settings for more information).
6. In config.yaml, the settings for running GISTIC2.0 and for benchmarking can be modified if necessary (see Settings for more information).
7. Run the pipeline shell script, which will create the required conda environment and run snakemake (recommended when snakemake is not installed yet):
```
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment