Commit 36bea04a authored by Beatrice Tan's avatar Beatrice Tan

Update README.md

parent 5696831c
......@@ -22,11 +22,12 @@ cd CNAprioritization
- 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:
- Leave all settings as default to use test dataset on SKCM tumor samples.
- Download Firehose data for tumor type of interest:
- Set cancer_type to tumor type abbreviation (see: https://gdac.broadinstitute.org/)
- Set date_data to "2016_07_15" to download the latest dataset or specify another date to use an older dataset (see: http://gdac.broadinstitute.org/runs/info/analyses__runs_list.html)
- 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:
- Set cancer_type to tumor type abbreviation (see https://gdac.broadinstitute.org/ for all options), e.g. "SKCM"
- 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).
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