Quality Control, Mapping and Reads Count for RNA-Seq Analysis

A cli for running multiple qsub jobs with HTSeq's htseq-count on a cluster.

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

Attempt at snakemake pipeline. Pyflow was forked from https://github.com/crazyhottom but the Snakefile infrastructure and rule calling was inspired by https://github.com/snakemake-workflows

SLURM job temps @UAlbany

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

Build Docker container for HTSeq and (optionally) convert to Apptainer/Singularity

RNA-seq QC benchmark (custom Python vs FastQC), adapter trimming, STAR alignment, and htseq-count-based strand-specificity analysis