RSP

A pipeline for analyzing RNAseq data

Developed in Institut Germans Trias i Pujol, high throughput genomics and bioinformatics department.

Description

RSP is a bioinformatic pipeline that maps and counts genomic variants from pair-end and single-end reads. It contains several modules.

• Prep: it creates three differnt folders:
  • Info: useful information about the files used, the parameters for the softwares have used.
  • Data: for each samples it will generate a folder
  • Report: what each module has done to samples
• QC : check input quality
• trimm : deletes the adapters. It will re-calculate the quality after this module
• Map : map the input reads to the reference genome
• Count: create a matix with the variants found in each sample

Softwares

This pipeline includes many open source software. In each module we can use:

• Map module: HISAT2, Salmon, Kallisto, STAR

Installation

RSP will require python v3.7 and java (we tested in openjdk 14 2020-03-17).

The RSP python pipeline will be available in pip and also available using conda.

RSP depends on multiple third party software that we have listed here [TODO: Add link].

We encourage you to install RSP and all dependencies using the conda environment we created and following these instructions.

To create a new conda environment, install third party software, install RSP and missing dependencies, do as follows:

1. Get requirements file from RSP git repo [TODO: Add link].

wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml

or available under the git repository in:

ls RNA_seq_pipe/RSP_pip/devel/conda/environment.yml

2. Create environment named RSP and install required packages using conda:

conda env create -f environment.yml

3. Activate environment and install RSP

## activate
conda activate RSP

## install latest python code
pip install RSP

Or install developer python code by doing:

## get git repo
git clone https://github.com/HCGB-IGTP/RNA_seq_pipe.git
cd RNA_seq_pipe/RSP_pip
sh devel/pypi/test_module.sh

To check everything is fine, try executing the config module:

RSP config

To additionally check RSP is working try to run a test example from https://github.com/griffithlab/rnaseq_tutorial

There are instructions to download this dataset within RSP git repository in:

cd toy_dataset/
sh get_toyDataset.sh
sh execute_test.sh

or available to download by executing the following command:

RSP test
sh execute_test.sh