/RNAseq

Preprocessing and differential expression analysis for QuantSeq 3' mRNA-seq data

Primary LanguageShellBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

RNAseq

LICENSE

If you use this tool, please cite us -

Paropkari AD, Bapat PS, Sindi SS, Nobile CJ. A
Computational Workflow for Analysis of 3' Tag-Seq Data. Curr Protoc. 
2023 Feb;3(2):e664. doi: 10.1002/cpz1.664. PMID: 36779816.

DESCRIPTION

This bash file that stiches together the preprocessing steps for raw RNA-seq data in FASTQ files from 3′RNA-seq project as well as outputs differential gene expression results.

The Wiki page provides detailed information about the using scripts in this repository.

MERCED SETUP

This pipeline is implemented on MERCED as a RNA-seq conda environment. MERCED users can log into MERCED and activate the environment to access the pipeline modules.

# activate RNA-seq conda evnvironment
source activate RNA-seq

LOCAL INSTALLATION

You can download this GitHub repository using the following command -

# Navigate to desired directory to download this folder on your machine

git clone https://github.com/akshayparopkari/RNAseq.git

Read more about creating the local Conda environment, required for running the workflow in section 3 of the Wiki.

# Making script files executable

cd RNAseq/

chmod u+x pipeline.sh

chmod u+x format_counts_table.py

USAGE and EXAMPLE

sh pipeline.sh [-h] inputs

OR

./pipeline.sh [-h] inputs

OPTIONS

inputs: Directory containing all raw RNA-seq FASTQ files

REFERENCES

  1. 3′RNA-seq - https://www.rna-seqblog.com/for-model-species-the-3-rna-seq-method-might-more-accurately-detect-differential-expression/
  2. BBTools Suite - https://jgi.doe.gov/data-and-tools/bbtools/
  3. FastQC - http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  4. STAR - https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

SCRIPT INFORMATION