Prediction of RNA-RNA contacts from RIC-seq data. Developed by Sergei Margasyuk ([email protected]) and Dmitri Pervouchine ([email protected]).

This package contains a pipeline for prediction of RNA-RNA contacts from RIC-seq data (Cai et al., 2020).

Clone this repository to your local system, into the place where you want to perform the data analysis.

git clone https://github.com/pervouchine/RIC-contacts.git
cd RIC-contacts

Configure the workflow according to your needs via editing the files in the config/ folder. Adjust config.yaml to configure the workflow execution, and samples.tsv to specify your sample setup.

Install Snakemake using conda:

# install mamba package manager if you don't have it
conda install -n base -c conda-forge mamba
conda create -c bioconda -c conda-forge -n snakemake snakemake

For installation details, see the instructions in the Snakemake documentation.

Activate the conda environment:

conda activate snakemake

Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores $N

using $N cores or run it in a cluster environment via

snakemake --use-conda --cluster qsub --jobs 100

or

snakemake --use-conda --drmaa --jobs 100

See the Snakemake documentation for further details.

To make a test run, type

make download
make test

The script will download a toy dataset (sample sheet, truncated fastq files, genome, and genome annotation confined to the first 100MB of chr1), unpack, update the config file, and execute the pipeline. The output files in results/test_hg19/test/contacts will be compared to those provided in the archive.

Download the RIC-seq files for HeLa cell line from GEO repository GSE127188. Download the control RNA-seq files from ENCODE consortium webpage.

The files are as follows:

  RNASeq_HeLa_total_rep1:
    - fastq/ENCFF000FOM.fastq
    - fastq/ENCFF000FOV.fastq
  RNASeq_HeLa_total_rep2:
    - fastq/ENCFF000FOK.fastq
    - fastq/ENCFF000FOY.fastq
  RIC-seq_HeLa_rRNA_depleted_rep1:
    - fastq/SRR8632820_1.fastq
    - fastq/SRR8632820_2.fastq
  RIC-seq_HeLa_rRNA_depleted_rep2:
    - fastq/SRR8632821_1.fastq
    - fastq/SRR8632821_2.fastq

The output of the pipeline consists of the following files:

• results/{genome}/{project}/{sample}/contacts is the list of contacts and their respective read counts in tsv format (columns 1-3 and 4-6 are the contacting coordinates, column 7 is read count).
• results/{genome}/{project}/views/global/contacts.bed is the BED12 file with contacts on the same chromosome and length less than the threshold defined in config. This file for HeLa experiment is available at 10.5281/zenodo.6511343.