Merge pull request #8 from aryeelab/dev

Update README.md

README.md

@@ -17,32 +17,33 @@ Simply run:
 
 # Usage example
 
-The example below uses the test dataset bundled with the `dnaloop` package source code. Download the package with:
+The example below uses the test dataset bundled with the `dnaloop` package source code. Download the package source with:
 
 `git clone https://github.com/aryeelab/dnaloop.git`
 
 
 1. Create a tab-separated sample description file with three columns:
 
-- Sample name
-- Read 1 FASTQ 
-- Read 2 FASTQ
+  - Sample name
+  - Read 1 FASTQ 
+  - Read 2 FASTQ
 
   For example:
-
-    $ cd dnaloop/test
-    $ cat samples.txt 
-    naive_esc_1     fastq/naive_esc_1.r1.fastq.gz   fastq/naive_esc_1.r2.fastq.gz
-    naive_esc_2     fastq/naive_esc_2.r1.fastq.gz   fastq/naive_esc_2.r2.fastq.gz
-    primed_esc_1    fastq/primed_esc_1.r1.fastq.gz  fastq/primed_esc_1.r2.fastq.gz
-    primed_esc_2    fastq/primed_esc_2.r1.fastq.gz  fastq/primed_esc_2.r2.fastq.gz
-
+  ```  
+  $ cd dnaloop/test
+  $ cat samples.txt 
+  naive_esc_1     fastq/naive_esc_1.r1.fastq.gz   fastq/naive_esc_1.r2.fastq.gz
+  naive_esc_2     fastq/naive_esc_2.r1.fastq.gz   fastq/naive_esc_2.r2.fastq.gz
+  primed_esc_1    fastq/primed_esc_1.r1.fastq.gz  fastq/primed_esc_1.r2.fastq.gz
+  primed_esc_2    fastq/primed_esc_2.r1.fastq.gz  fastq/primed_esc_2.r2.fastq.gz
+  ```
+
   Note that the FASTQ columns (2 and 3) can contain a comma-separated list of FASTQs. This is commonly the case when a sample is sequenced multiple times.
 
 2. Run the pipeline:
-
-    $ preprocess_chiapet --out naive_vs_primed --bwa-index ./test_genome.fa samples.txt
-
+  ```  
+  $ preprocess_chiapet --out naive_vs_primed --bwa-index ./test_genome.fa samples.txt
+  ```
 
 # Usage details
 
@@ -55,4 +56,4 @@ The example below uses the test dataset bundled with the `dnaloop` package sourc
       --out TEXT         Output directory name  [required]
       --bwa-index TEXT   BWA index location  [required]
       --keep-temp-files  Keep temporary files?
-      --help             Show this message and exit.
+      --help             Show this message and exit.