Updated rST

README.md

@@ -5,26 +5,26 @@ Pipelines for analyzing padlock-captured DNA sequencing data
 
 
 
-1) Initial configuration:
+## 1. Initial configuration:
 
 
-a) Install necessary scripts (bowtie, bismark, trimmomatic):
+### - Install necessary scripts (bowtie, bismark, trimmomatic):
 
   `$ make install`
 
-b) 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 (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/`