From c86a62b7f221febe28ad33f7c1deae3d4574fab8 Mon Sep 17 00:00:00 2001
From: Orion Buske <buske@cs.toronto.edu>
Date: Sat, 8 Nov 2014 18:47:32 -0500
Subject: [PATCH] Updated README and renamed pipeline script

---
 README.md                                     | 21 +++++++++++++--------
 src/bis_seq/{run_bismark.sh => run_sample.sh} |  0
 2 files changed, 13 insertions(+), 8 deletions(-)
 rename src/bis_seq/{run_bismark.sh => run_sample.sh} (100%)

diff --git a/README.md b/README.md
index 1c4c6ff..5c2ce9e 100644
--- a/README.md
+++ b/README.md
@@ -5,20 +5,25 @@ Pipelines for analyzing padlock-captured DNA sequencing data
 
 
 
-Initial configuration:
+1) Initial configuration:
 
-1) Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them)
 
-  e.g. `$ mkdir sequences/hg19; cd sequences/hg19; wget ....fq.gz`
+a) Install necessary scripts (bowtie, bismark, trimmomatic):
 
-2) Prepare bismark genomic indexes:
+  `$ make install`
 
-  e.g. `$ lib/bismark_v0.12.3/bismark_genome_preparation refs/hg19`
+b) Reference preparation:
 
-3) Install necessary scripts:
+- Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them)
 
-  `$ make install`
+  e.g. `$ mkdir sequences/hg19; cd sequences/hg19; ln -s /path/to/hg19.fa`
+
+- Prepare bismark genomic indexes:
+
+  `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/phiX`
+  `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19`
 
 
-Running a sample:
+2) Running a sample:
 
+  `$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`
diff --git a/src/bis_seq/run_bismark.sh b/src/bis_seq/run_sample.sh
similarity index 100%
rename from src/bis_seq/run_bismark.sh
rename to src/bis_seq/run_sample.sh