Initial commit

README.md

+# Strand-seq pipeline
+
+Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https://bitbucket.org/snakemake/snakemake) pipeline.
+
+### How to use it
+
+  1. **Install required software:**
+  
+    * Install [mosaicatcher](https://github.com/friendsofstrandseq/mosaicatcher) (*currently you will need the `develop` branch*)
+    * Get the R-scripts from [strandsequtils](https://github.com/friendsofstrandseq/strandsequtils)
+  
+  2. **Set up the configuration of the smakemake pipeline**
+  
+    * Open `Snake.config.json` and specify the path to the executatables (such as Mosaicatcher) and to the R scripts.
+    * Create a subdirectory `bam` and copy (or soft-link) the Strand-seq single-cell libraries in there. Note that bam files need to contain a read group and should have duplicates marked.
+   
+  3. **Run Snakemake**
+
+    * run `snakemake` to compute all tasks locally
+    * Alternatively, you can ask Snakemake to submit your jobs to a HPC cluster. To this end edit the `Snake.cluster.json` file according to your available HPC environment and call 
+      
+      ```
+      snakemake -j 100 \
+        --cluster-config Snake.cluster.json \
+        --cluster "???"
+      ```