Reads were aligned to reference (GRCh38) with ‘STAR’ (v2.7.2b).
Gene counts were quantified with ‘FeatureCounts’ (v1.6.4).
Differential gene expression analysis was performed using the R package ‘DEseq2’(v1.26).
GSEA statistical analysis was carried out with the R package ‘fgsea’ (v1.14.0).
12/08/2020: Added handling of short read alignment 03/02/2021: Added STAR gene counts 06/29/2021: Clarified documentation in a number of places 01/25/2022: Writing stderr and stdout to job folders
In this folder
design4expression.py -> job_expression.pl (expression.pl) -> summarize4expression.py -> DE.r
File: example.sh
Description: This shell script is an example job submission script to be used by job_expression.pl
File: design4expression.py
Description: This python3 script take samples from manifest file, and create two design files, one for job_expression.pl, another for summarize4expression.py
File: job_expression.pl
Description: This perl script is a wrapper around expression.pl for easy submission of the expression analysis jobs
File: expression.pl
Description: This perl script executes QC, alignment, and counting for raw RNA-seq data
File: summarize4expression.py
Description: This python3 script examines the output from expression.pl for all analyzed samples, and summarizes the expression data into a matrix table
File: DE.r
Description: This R script takes the output of summarize4expression.py and performs regular RNA differential analyses
Folder: script
Description: This folder stores dependency scripts for the main scripts
Folder: example_data
Description: This folder stores example input data for the pipeline
Folder: results
Description: This folder stores the example output of the pipeline