From 5a2d5106c45b000539db38dea2b29f464931943e Mon Sep 17 00:00:00 2001
From: Orion Buske <buske@cs.toronto.edu>
Date: Sat, 8 Nov 2014 18:50:12 -0500
Subject: [PATCH] Clarified instructions

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 5c2ce9e..232569e 100644
--- a/README.md
+++ b/README.md
@@ -24,6 +24,8 @@ b) Reference preparation:
   `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19`
 
 
-2) Running a sample:
+2) Run pipeline on a sample directory (containing paired-end files of the form: `<SAMPLE>_L001_R1_001.fastq.gz`, `<SAMPLE>_L001_R2_001.fastq.gz`):
 
   `$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`
+
+  - Expects files within the directory of the form: