Parallelized RNA-seq analysis pipeline

Installation

1. Download zip and extract to root of your working directory OR Clone repo to your working diectory.
2. chomd +x bash_script.sh

Use

1. Copy/move all your fastq files to root of your working directory.
2. If running stand alone, install the following together with their dependencies: fastqc, multiqc, flexbar(v3.x), hisat2 (v2.x.x), samtools, htseq and gnu-parallel. If running in HPC, make sure the modules are available.
3. To generate raw transcript count tables, run bash_script.sh OR submit batch to SLURM. Run standalone as ./bash_script.sh <link to reference genome> <link to anotation> <reference identifier> If runnning in HPC, update the arguments in batch file and sbatch batch. Compressed GZ file links are expected for reference genome and annotation.
4. Use R_script.rmd to do differential expression and enrichment analysis. All necssary packages are available in CRAN, Github, or Bioconductor and will be installed by the script if necessary.

Detail

Activity	Software
Alignment	HISAT2
Abundance	HTSeq
Differential expression	DESeq2
Enrichement	Clusterprofiler

Citation

Sharma A, Ference CM, Shantharaj D, Baldwin EA, Manthey JA, Jones JB. 2022. Transcriptomic analysis of changes in Citrus × microcarpa gene expression post Xanthomonas citri subsp. citri infection. European Journal of Plant Pathology 162:163–181. doi: http://dx.doi.org/10.1007/s10658-021-02394-6.