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Detect loops (and other patterns) in Hi-C contact maps.

Project description

Chromosight

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Detect chromatin loops (and other patterns) in Hi-C contact maps.

Installation

pip3 install -U chromosight

or, if you want to get the very latest version:

sudo pip3 install -e git+https://github.com/koszullab/chromosight.git@master#egg=chromosight

Usage

chromosight detect <contact_maps> [<output>] [--kernels=None] [--loops]
                       [--borders] [--precision=4] [--iterations=auto]
                       [--output]

Input

Input Hi-C contact maps can be either in bedgraph2d or cool format. Bedgraph2d is defined as a tab-separated text file with 7 columns: chr1 start1 end1 chr2 start2 end2 contacts. The cool format is an efficient and compact format for Hi-C data based on HDF5. It is maintained by the Mirny lab and documented here: https://mirnylab.github.io/cooler/

Output

Two files are generated in the output directory (replace pattern by the pattern used, e.g. loops or borders):

  • pattern.txt: List of genomic coordinates, bin ids and correlation scores for the pattern identified
  • pattern.json: JSON file containing the windows (of the same size as the kernel used) around the patterns from pattern.txt

Options

Pattern exploration and detection

Explore and detect patterns (loops, borders, centromeres, etc.) in Hi-C contact
maps with pattern matching.

Usage:
    chromosight detect <contact_map> [<output>] [--kernel-config FILE]
                        [--pattern=loops] [--precision=auto] [--iterations=auto]
                        [--win-fmt={json,npy}] [--subsample=no]
                        [--inter] [--max-dist=auto] [--no-plotting] [--threads 1]
    chromosight generate-config <prefix> [--preset loops]

    detect: 
        performs pattern detection on a Hi-C contact map using kernel convolution
    generate-config:
        Generate pre-filled config files to use for `chromosight detect`. 
        A config consists of a JSON file describing analysis parameters for the
        detection and path pointing to kernel matrices files. Those matrices
        files are tsv files with numeric values ordered in a square dense matrix
        to use for convolution.

Arguments for detect:
    -h, --help                  Display this help message.
    --version                   Display the program's current version.
    contact_map                 The Hi-C contact map to detect patterns on, in
                                bedgraph2d or cool format. 
    output                      name of the output directory
    -I, --inter                 Enable to consider interchromosomal contacts.
    -i, --iterations auto       How many iterations to perform after the first
                                template-based pass. Auto sets an appropriate
                                value loaded from the kernel configuration
                                file. [default: auto]
    -k, --kernel-config FILE    Optionally give a path to a custom JSON kernel
                                config path. Use this to override pattern if 
                                you do not want to use one of the preset 
                                patterns.
    -m, --max-dist auto         Maximum distance from the diagonal (in base pairs)
                                at which pattern detection should operate. Auto
                                sets a value based on the kernel configuration
                                file and the signal to noise ratio. [default: auto]
    -n, --no-plotting           Disable generation of pileup plots.
    -P, --pattern loops         Which pattern to detect. This will use preset
                                configurations for the given pattern. Possible
                                values are: loops, borders, hairpin. [default: loops]
    -p, --precision auto        Precision threshold when assessing pattern
                                probability in the contact map. A lesser value
                                leads to potentially more detections, but more
                                false positives. [default: auto]
    -s, --subsample=INT         Subsample contacts from the matrix to INT contacts.
                                This is useful when comparing matrices with different
                                coverages. [default: no]
    -t, --threads 1             Number of CPUs to use in parallel. [default: 1]
    -w, --win-fmt={json,npy}    File format used to store individual windows
                                around each pattern. Window order match
                                patterns inside the associated text file.
                                Possible formats are json and npy. [default: json]

Arguments for generate-config:
    prefix                      Path prefix for config files. If prefix is a/b,
                                files a/b.json and a/b.1.txt will be generated.
                                If a given pattern has N kernel matrices, N txt
                                files are created they will be named a/b.[1-N].txt.
    -p, --preset loops          Generate a preset config for the given pattern.
                                Preset configs available are "loops" and 
                                "borders". [default: loops]

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