From e725295054a19b5a4005c7f555c651e570fe80d1 Mon Sep 17 00:00:00 2001 From: Orion Buske Date: Sat, 8 Nov 2014 18:59:39 -0500 Subject: [PATCH] Updated rST --- README.md | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 96d6a72..d9246c1 100644 --- a/README.md +++ b/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: `_L001_R1_001.fastq.gz`, `_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: `_L001_R1_001.fastq.gz`, `_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/`