padlock-pipeline

Pipelines for analyzing padlock-captured DNA sequencing data

1. Initial configuration:

a) Install necessary scripts (bowtie, bismark, trimmomatic):

$ make install

b) 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 (containing paired-end files of the form: <SAMPLE>_L001_R1_001.fastq.gz, <SAMPLE>_L001_R2_001.fastq.gz):

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

• Expects files within the directory of the form: