Spectral decomposition for characterizing long-range interaction profiles in Hi-C maps

Related tags

Geolocationinspectral
Overview

Inspectral

Spectral decomposition for characterizing long-range interaction profiles in Hi-C maps.

Snakemake workflow for the unsupervised method presented in Spracklin, Abdennur et al., 2021.

Steps

  1. Place supplementary bigwig file information in config/track_metadata.tsv to include in graphical outputs. Must be tab-delimited, including header. Must have columns:
  • Name: a display name
  • ID: a unique identifier to use in the database (can be the same as Name)
  • FileFormat: must be the string bigWig
  • Path: a local path to the file

  1. Edit config.yaml.

  2. Run:

# Generate pre-aggregated supplementary bigwig tracks if provided
$ snakemake make_track_db --force --cores all

# Run the pipeline
$ snakemake --cores all
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Comments
  • iterative correction bug in inspectro

    iterative correction bug in inspectro

    After installing inspectro from environment file the rule eigdecomp has failed with this error: image

    Upgrading cooltools (installed locally from GitHub) and changing the import in eigendecomposition script (from cooltools.api.eigdecomp import _filter_heatmap, _fake_cis) fixes it.

    opened by agalitsyna 1
  • Inspectro module

    Inspectro module

    Technical improvements:

    • pyproject.toml allows installing inspectro system-wide
    • instructions for installation updated
    • Snakemake runs pip-installed inspectro instead of local "utils" module

    Functionality improvement:

    • cis decomposition added (both utils and Snakemake)
    • config option to run either cis or trans eigdecomp
    • projection function added to utils module

    Small improvements:

    • Docs improvements and code structure fixes in utils
    opened by agalitsyna 0
  • Eigen Decompsition

    Eigen Decompsition

    I was trying the pipeline with HT1080 HI-C data (.mcool generated from distiller.nf). Unfortunately, eigdecomp rule never worked. I think it is the problem with partition. I am sending you my SRA code (SRR7586416, SRR7586418). Please tell me what to do.

    opened by Sen0108 16
Releases(v0.1.1)
Owner
Nezar Abdennur
Nezar Abdennur
GitHub Repository
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