padlock-pipeline

Pipelines for analyzing padlock-captured DNA sequencing data

1. Initial configuration:

Install necessary scripts (bowtie, bismark, trimmomatic):

`$ make install`

Reference preparation:

* 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`

* Prepare bismark genomic indexes:

    `$ 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)

Pipeline can then be run with SGE-compatible command:

  `$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`