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/