buske/padlock-pipeline

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Nov 6, 2014 Initial commit
	1	padlock-pipeline
	2	================
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	4	Pipelines for analyzing padlock-captured DNA sequencing data
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	8	### 1. Initial configuration:
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	11	#### Install necessary scripts (bowtie, bismark, trimmomatic):
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	13	make install
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	15	#### Reference preparation:
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	17	* Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them), e.g.:
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	19	mkdir sequences/hg19
	20	cd sequences/hg19
	21	ln -s /path/to/hg19.fa
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	23	* Prepare bismark genomic indexes:
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	25	lib/bismark_v0.12.3/bismark_genome_preparation sequences/phiX
	26	lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19
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	29	### 2. Run pipeline on a sample directory
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	31	Sample directory should contain paired-end files of the form: `<SAMPLE>_L001_R1_001.fastq.gz`, `<SAMPLE>_L001_R2_001.fastq.gz`)
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	33	Pipeline can then be run with SGE-compatible command:
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	35	src/bis_seq/run_sample.sh hg19 /path/to/sample/