danydoerr/hifive_workflow

HiFive Workflow

Description

This is a snakemake workflow to normalize Hi-C matrices by genomic distance using HiFive

Installation

• Make sure you have conda installed.

• Then create two environments to run the pipeline:

  1. Workflow environment:

     conda env create -n hic-workflow --file conda-workflow.lst
     

  2. HiFive Py2 environment:

     conda env create -n hic-hifive --file conda-hifive.lst
     

Running the pipeline

• Activate the workflow environment:

  conda activate hic-workflow
  

• Create alias for snakemake so that it remains accessible even if environment is unloaded:

  alias snakemake=$(which snakemake)
  

• Edit config.yaml to

  1. specify samtools binary in samtools_bin (you can find this out by typing which samtools)
  2. adjust min_interactions that indicates the minimum number of ditags between two genomic regions so that they are considered to be interacting with each other (you can specify multiple thresholds, which is encouraged)
  3. adjust resolution that determines the coarseness of the hic-map (you can specify here multiple resolutions which is encouraged)
  4. adjust super_resolution_factors that smoothes the matrix by taking into account the ditags of neighboring genomic regions (you can specify multiple factors which is encouraged)

• Create dataset.cfg

  1. Copy template: cp dataset.cfg.template dataset.cfg
  2. Fill out the settings in [global], then create entries for each replicate/condition, each time specifying the paths for read pair 1 & 2.

• Load HiFive environment:

  conda activate hic-hifive
  

• Run snakemake:

  snakemake -j<number of threads you can afford>