{ "cells": [ { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Using Higashi software suite for scHi-C analysis\n", "\n", "**Note:** Change the path of the files accordingly!" ] }, { "cell_type": "markdown", "metadata": { "pycharm": { "name": "#%% md\n" }, "slideshow": { "slide_type": "slide" } }, "source": [ "# Step I: Install the packages\n", "Copy the code block below and run it in the terminal. \n", "Some GPU related packages are recommended to be installed in advance:\n", "- pytorch\n", "- py3nvml" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "pycharm": { "name": "#%%\n" }, "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "git clone https://github.com/ma-compbio/Higashi\n", "cd Higashi\n", "python setup.py install\n", "cd ../\n", "git clone https://github.com/ma-compbio/Fast-Higashi\n", "cd Fast-Higashi\n", "python setup.py install\n", "cd ../" ] }, { "cell_type": "markdown", "metadata": { "pycharm": { "name": "#%% md\n" }, "slideshow": { "slide_type": "slide" } }, "source": [ "# Step II: Prepare the input files\n", "\n", "In this tutorial, we'll use the Lee et al. sn-m3c-seq dataset on human prefrontal cortex (PFC). \n", "Higashi software is compatible with two types of input format\n", "\n", "**Format 1 (higashi_v1)**\n", "\n", "You'll need two files:\n", "- label_info.pickle (stores cell meta-information)\n", "- data.txt (stores all the single cell contacts)\n", "\n", "The label_info.pickle file can be generated via the following code." ] }, { "cell_type": "code", "execution_count": null, "metadata": { "pycharm": { "name": "#%%\n" }, "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "import pickle\n", "import numpy as np\n", "\n", "label_info = {'name': np.arange(1000),\n", " 'age': np.ones(1000),\n", " }\n", "\n", "pickle.dump(label_info, open(\"./label_info.pickle\", \"wb\"))" ] }, { "cell_type": "markdown", "metadata": { "pycharm": { "name": "#%% md\n" }, "slideshow": { "slide_type": "slide" } }, "source": [ "As for the data.txt file, here's an example to give you an idea of the structure: " ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "pycharm": { "name": "#%%\n" }, "slideshow": { "slide_type": "fragment" } }, "outputs": [ { "data": { "text/html": [ "
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