From cda6fd8366d0a09520f6de5be284053acb8155c6 Mon Sep 17 00:00:00 2001 From: Nils Wagner Date: Fri, 10 Feb 2023 14:48:57 +0100 Subject: [PATCH] initial commit --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 8efef2a..2be1e76 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ # AbSplice analysis -Repository for all preprocessing and analyses done in the paper "Aberrant splicing across human tissues" +Repository for the analyses done in the paper "Aberrant splicing across human tissues" # Folder Structure -The project is setup as a snakemake pipeline. +The project is setup as a snakemake pipeline. -* The `workflow` folder contains the config files and all the analysis scripts. +* The `workflow` folder contains the config files and the analysis scripts for each dataset. * `config` contains yaml files for the GTEx, mito and ALS datasets, as well as a yaml that defines the file structure used in all analysis. - * `scripts` contains all processing and analysis scripts. The `common` folder contains all scripts shared acorss datasets. `gtex_v8`, `mito` and `als` contain analysis scripts specific to the respective dataset. + * `scripts` contains all processing and analysis scripts. The `common` folder contains all scripts shared acorss datasets. `gtex_v8`, `mito` and `als` contain analysis scripts specific to the respective dataset. Each of the dataset folders contains a Snakefile that runs the analysis of the respective dataset. As mito and als depend on gtex_v8 results (e.g. AbSplice model, SpliceMaps from GTEx tissues), the gtex_v8 Snakefile needs to be executed first. # Overview of the analysis pipeline In `scripts/common` most of the scripts of the pipeline are included.