From 842f1f95ab4a6d139f8a8c9182c802cf480689e6 Mon Sep 17 00:00:00 2001 From: Ryo Kita Date: Mon, 23 Jul 2018 17:31:16 -0700 Subject: [PATCH 1/2] updated readme to include additional points to change .cfg file and also instruction to download collection --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index b6ce120..c1edb18 100644 --- a/README.md +++ b/README.md @@ -26,6 +26,11 @@ 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`) + * 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 2. 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). From 9a398bb082c7b48977f51472ae1f902392fa5a21 Mon Sep 17 00:00:00 2001 From: Ryo Kita Date: Mon, 23 Jul 2018 17:35:34 -0700 Subject: [PATCH 2/2] Changed the numbers in the bullets --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c1edb18..b4f99ae 100644 --- a/README.md +++ b/README.md @@ -31,9 +31,9 @@ The following steps outline how to test run DEPICT on LDL cholesterol GWAS summa 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 -2. Run DEPICT on the LDL summary statistics +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`