/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%
Perl Shell Python Makefile

Clone with HTTPS

Use Git or checkout with SVN using the web URL.

Download ZIP
Find file
Switch branches/tags
Nothing to show
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
.gitignore
LICENSE
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: