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README.md

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 # 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.