dnaloop

A preprocessing and QC pipeline for ChIA-PET data.

Dependencies

The following dependencies need to be manually installed:

• samtools
• bedtools
• bwa

Installation

Simply run:

$ pip install dnaloop

Usage example

The example below uses the test dataset bundled with the dnaloop package source code. Download the package with:

git clone https://github.com/aryeelab/dnaloop.git

1. Create a sample description file:

Sample description files can be created in one of two formats:

• .txt for simple cases where there is a single FASTQ pair per sample.
• .yaml for cases where individual samples may have one or more FASTQ pairs associated with it. This is typically the case when a library is sequenced more than once (e.g. 2+ runs or 2+ lanes).

Option 1: .txt format

Create a tab-separated sample description file with three columns:

• Sample name
• Read 1 FASTQ
• Read 2 FASTQ

For example:

$ cd dnaloop/test
$ cat samples.txt 
naive_esc_1     fastq/naive_esc_1.r1.fastq.gz   fastq/naive_esc_1.r2.fastq.gz
naive_esc_2     fastq/naive_esc_2.r1.fastq.gz   fastq/naive_esc_2.r2.fastq.gz
primed_esc_1    fastq/primed_esc_1.r1.fastq.gz  fastq/primed_esc_1.r2.fastq.gz
primed_esc_2    fastq/primed_esc_2.r1.fastq.gz  fastq/primed_esc_2.r2.fastq.gz

Option 2: .yaml format

Example yaml format sample description file:

samples:
   naive_esc: 
     - fastq/naive_esc_1.r1.fastq.gz fastq/naive_esc_1.r2.fastq.gz
     - fastq/naive_esc_2.r1.fastq.gz fastq/naive_esc_2.r2.fastq.gz
   primed_esc:
     - fastq/primed_esc_1.r1.fastq.gz fastq/primed_esc_1.r2.fastq.gz

In this example the naive_esc sample has two FASTQ pairs (probably from two separate sequencing runs, or two different lanes). The second sample (primed_esc) has only one FASTQ pair.

2. Run the pipeline:

$ preprocess_chiapet --out naive_vs_primed --bwa-index ./test_genome.fa samples.txt

Usage details

$ preprocess_chiapet --help
Usage: preprocess_chiapet [OPTIONS] MANIFEST

A preprocessing and QC pipeline for ChIA-PET data.

Options:
  --out TEXT         Output directory name  [required]
  --bwa-index TEXT   BWA index location  [required]
  --peak-pad TEXT    Peak padding width (applied on both left and right)
  --merge-gap TEXT   Max gap size for merging peaks
  --use-lsf          Submit jobs to an LSF cluster?
  --bsub-opts TEXT   LSF bsub options
  --keep-temp-files  Keep temporary files?
  --no-qc-report     Skip QC report generation? (Requires R)
  --help             Show this message and exit.