Updated rST

README.md

@@ -5,27 +5,29 @@ Pipelines for analyzing padlock-captured DNA sequencing data
 
 
 
-## 1. Initial configuration:
+### 1. Initial configuration:
 
 
-### - Install necessary scripts (bowtie, bismark, trimmomatic):
+#### Install necessary scripts (bowtie, bismark, trimmomatic):
 
-  `$ make install`
+    `$ make install`
 
-### - Reference preparation:
+#### Reference preparation:
 
-  * Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them)
+    * Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them)
 
-    e.g. `$ mkdir sequences/hg19; cd sequences/hg19; ln -s /path/to/hg19.fa`
+        e.g. `$ mkdir sequences/hg19; cd sequences/hg19; ln -s /path/to/hg19.fa`
 
-  * Prepare bismark genomic indexes:
+    * Prepare bismark genomic indexes:
 
-    `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/phiX`
-    `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19`
+        `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/phiX`
+        `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19`
 
 
-## 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`):
+### 2. Run pipeline on a sample directory
 
-  `$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`
+  Sample directory should contain paired-end files of the form: `<SAMPLE>_L001_R1_001.fastq.gz`, `<SAMPLE>_L001_R2_001.fastq.gz`)
 
-  - Expects files within the directory of the form: 
+  Pipeline can then be run with SGE-compatible command:
+
+      `$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`