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/