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CAUTION: hard-coding of chromosome.
Sascha Meiers authored 
TODO: a dynamic rule for chromosomes would be more elegant here, but I have trouble getting it to work
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utils
.gitignore
README.md
Snake.config.json
Snakefile
README.md

Strand-seq pipeline

Ongoing work

Preliminary SV calling using Strand-seq data - summarized in a 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)
* Install [Strand-Phaser](https://github.com/daewoooo/StrandPhaseR)
  1. 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.
  1. 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 "???"
  ```