Guttman_Ismagilov_Labs

This github repository includes single-cell SPRITE automatic bioinformatic pipeline (Snakemake workflow) to process mouse scSPRITE data for a research paper XYZ.

The original SPRITE technique has been documented in this paper Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.

This Snakemake workflow has been tested under Centos7 environment with proper pre-installation of necessary software tools.

Installation guide:

• Pre-install the following software tools:
  • STAR (generate STAR index for the genome of your interest);
  • samtools
  • bedtools2
  • fastqc
  • Hi-Corrector
• Install scSPRITE source codes git clone https:/caltech-bioinformatics-resource-center/Guttman_Ismagilov_Labs.git. Modify config.yaml file with local PATH information for STAR, STAR index, samtools, bedtools2, fastqc and Hi-Corrector.

Quick run:

• Relocate to local scSPRITE directory:
• cd scSPRITE
• Transfer raw paired-end fastq files (xxx1.fq.gz, xxx2.fq.gz) to raw_fastq directory:
• cp ~/data/*1.fq.gz raw_fastq/ cp ~/data/*2.fq.gz raw_fastq/
• Try a snakemake dry run:
• snakemake -n
• If no error message, perform first step snakemake run with multi cores (e.g., 4 cores):
• snakemake --cores 4
• If no error message, do second step snakemake run with multi cores （e.g., 4 cores):
• snakemake -s Snakefile_contact_heatmap --cores 4

Directory contents

• scSPRITE: A folder with Snakemake workflow scripts to process single-cell SPRITE data.