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Updated readme to include additional points to change in .cfg #12

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updated readme to include additional points to change .cfg file and a…
rkita Jul 24, 2018
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Changed the numbers in the bullets
rkita Jul 24, 2018
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9 changes: 7 additions & 2 deletions README.md
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Expand Up @@ -26,9 +26,14 @@ The following steps outline how to test run DEPICT on LDL cholesterol GWAS summa

1. Edit `DEPICT/example/ldl_teslovich_nature2010.cfg`
* Point `plink_executable` to where PLINK executable (version 1.9 or higher) is on our system (e.g. `/usr/bin/plink`)
2. Run DEPICT on the LDL summary statistics
* Point `analysis_path` to absolute path where output files will be written
* Point `gwas_summary_statistics_file` to absolute path to gwas summary statistics in the example directory.
2. Download the collections file.
* Download the collections file and place in `data/collections/ld0.5_collection_1000genomespilot_depict_150429.txt.gz`
* The files is located in https://data.broadinstitute.org/mpg/depict/depict_download/collections/ld0.5_collection_1000genomespilot_depict_150429.txt.gz
3. Run DEPICT on the LDL summary statistics
* E.g. `./src/python/depict.py example/ldl_teslovich_nature2010.cfg`
3. Investigate the results (see the [Wiki](https://github.com/perslab/DEPICT/wiki) for a description of the output format).
4. Investigate the results (see the [Wiki](https://github.com/perslab/DEPICT/wiki) for a description of the output format).
* DEPICT loci `ldl_teslovich_nature2010_loci.txt`
* Gene prioritization results `ldl_teslovich_nature2010_geneprioritization.txt`
* Gene set enrichment results `ldl_teslovich_nature2010_genesetenrichment.txt`
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