/padlock-pipeline

Analysis pipeline for DNA methylation profiling using padlock bisulfite sequencing, based on the Bismark tool.
  1. Perl 55.4%
  2. Shell 22.1%
  3. Python 20.2%
  4. Makefile 2.3%
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lib
sequences
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Makefile
README.md

README.md

padlock-pipeline

Pipelines for analyzing padlock-captured DNA sequencing data

Initial configuration:

  1. Download fasta files for reference genome into subdirectory of sequences folder (or symlink them)

e.g. $ mkdir sequences/hg19; cd sequences/hg19; wget ....fq.gz

  1. Prepare bismark genomic indexes:

e.g. $ lib/bismark_v0.12.3/bismark_genome_preparation refs/hg19

  1. Install necessary scripts:

$ make install

Running a sample: