RNAseq

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.

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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

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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

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USAGE and EXAMPLE

sh pipeline.sh [-h] inputs

OR

./pipeline.sh [-h] inputs

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OPTIONS

inputs: Directory containing all raw RNA-seq FASTQ files

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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

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SCRIPT INFORMATION

• VERSION: 0.0.6
• AUTHOR: Akshay Paropkari
• LICENSE: BSD 3-Clause License