5.1. Experiment Configuration file

This file contains all the needed configuration to run an experiment. It’s used by SnakeMake as well as the scripts. It’s a standard YAML formatted file.


All path shall end with a /

Here is the content of config/sample.yaml that shows all available configuration keys with a lot of comments. In this sample, we have three species (suitably named Species1, Species2 and Species3), and two Hi-C resolutions (10kb and 20kb).

# sample.yaml

# Sample config file.

# WARNING: all path shall end with a /

# Where are the scripts?
bin: "/path/to/python/scripts"

# Activate a conda environment. If not needed, leave empty
condacmd: "source /path/to/conda/bin/activate myenv"

# The path to the root directory for the results (holds multiple experiments)
rootdir: "/path/to/rootdir"

# The experiment name
experiment: "myexpe"

# The path to the TSV with all the orthologs
orthologs: "/path/to/the/orthologs.tsv"

# The method for joining pairs, exactly one of "union", "intersection" or
# "atLeastTwo. See the documentation for more information.
method: "union"

# Will we exclude pairs with both values lesser than or equal to the threshold?
exclude: false

# The Hi-C resolutions
resolutions: ["10kb", "20kb"]

# Let's talk about data...

  # The first dataset, "Species1" will be used as dataset name in the results
    # Its genes, in BED format
    genes: "/path/to/sp1/genes.bed"
    # The different directories for the Hi-C, one directory per resolutions
      # The keys are the resolutions, and the values the paths
      10kb: "/path/to/hic/at/10kb/"
      20kb: "/path/to/hic/at/20kb/"

  # Idem for the other datasets

    genes: "/path/to/sp2/genes.bed"
      10kb: "/path/to/sp2/hic/at/10kb/"
      20kb: "/path/to/sp2/hic/at/20kb/"

    genes: "/path/to/sp3/genes.bed"
      10kb: "/path/to/sp3/hic/at/10kb/"
      20kb: "/path/to/sp3/hic/at/20kb/"