Updated rST

README.md

@@ -10,24 +10,26 @@ Pipelines for analyzing padlock-captured DNA sequencing data
 
 #### Install necessary scripts (bowtie, bismark, trimmomatic):
 
-    `$ make install`
+    make install
 
 #### 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.:
 
-        e.g. `$ mkdir sequences/hg19; cd sequences/hg19; ln -s /path/to/hg19.fa`
+    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
 
-  Sample directory should contain paired-end files of the form: `<SAMPLE>_L001_R1_001.fastq.gz`, `<SAMPLE>_L001_R2_001.fastq.gz`)
+Sample directory should contain paired-end files of the form: `<SAMPLE>_L001_R1_001.fastq.gz`, `<SAMPLE>_L001_R2_001.fastq.gz`)
 
-  Pipeline can then be run with SGE-compatible command:
+Pipeline can then be run with SGE-compatible command:
 
-      `$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`
+    src/bis_seq/run_sample.sh hg19 /path/to/sample/