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

Last update: Dec 13, 2022

Related tags

Geolocation inspectral

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

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

Edit config.yaml.
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

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

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
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

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)

v0.1.1(Dec 13, 2022)

Fix numba issue by upgrading cooltools #2.
Source code(tar.gz)
Source code(zip)

Owner

Nezar Abdennur

GitHub Repository

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

Related tags

Overview

Inspectral

Steps

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