From 2ba988b60d1ea052f5e126b6a09dd125f4929133 Mon Sep 17 00:00:00 2001
From: Orion Buske <buske@cs.toronto.edu>
Date: Fri, 7 Nov 2014 02:03:39 -0500
Subject: [PATCH] Initial commit with .gitignore

---
 .gitignore |  1 +
 README.md  | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..e4e5f6c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+*~
\ No newline at end of file
diff --git a/README.md b/README.md
index 7bb4bc9..1c4c6ff 100644
--- a/README.md
+++ b/README.md
@@ -2,3 +2,23 @@ padlock-pipeline
 ================
 
 Pipelines for analyzing padlock-captured DNA sequencing data
+
+
+
+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`
+
+2) Prepare bismark genomic indexes:
+
+  e.g. `$ lib/bismark_v0.12.3/bismark_genome_preparation refs/hg19`
+
+3) Install necessary scripts:
+
+  `$ make install`
+
+
+Running a sample:
+