From b56d81f0eae38932c62e7e17f229ef5a5bb1c094 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Thu, 11 Jan 2018 13:52:54 +0100
Subject: [PATCH] Explain that multiple samples can be run now
---
README.md | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/README.md b/README.md
index 73a2edb..3c82929 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@ Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https
### 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 BSgenome.Hsapiens.UCSC.hg38:
@@ -18,15 +18,20 @@ Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https
* [Strand-Phaser](https://github.com/daewoooo/StrandPhaseR) is installed automagically
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.
-
+
+ * Open `Snake.config.json` and specify the path to the executatables
+ (such as Mosaicatcher) and to the R scripts.
+ * Create a subdirectory `bam/` and another subdirectory per sample (e.g.
+ `bam/NA12878`). **Multiple samples can be run together not**.
+ Then copy (or soft-link) the Strand-seq single-cell libraries (one BAM
+ file per cell) 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
-
+ * 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 \
--
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