Updated README and renamed pipeline script

README.md

@@ -5,20 +5,25 @@ Pipelines for analyzing padlock-captured DNA sequencing data
 
 
 
-Initial configuration:
+1) Initial configuration:
 
-1) Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them)
 
-  e.g. `$ mkdir sequences/hg19; cd sequences/hg19; wget ....fq.gz`
+a) Install necessary scripts (bowtie, bismark, trimmomatic):
 
-2) Prepare bismark genomic indexes:
+  `$ make install`
 
-  e.g. `$ lib/bismark_v0.12.3/bismark_genome_preparation refs/hg19`
+b) Reference preparation:
 
-3) Install necessary scripts:
+- Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them)
 
-  `$ make install`
+  e.g. `$ mkdir sequences/hg19; cd sequences/hg19; ln -s /path/to/hg19.fa`
+
+- Prepare bismark genomic indexes:
+
+  `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/phiX`
+  `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19`
 
 
-Running a sample:
+2) Running a sample:
 
+  `$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`