FastqToGenCounts: Converting Fastq Files to Gene Counts Matrices

Abstract FastqToGeneCounts is a computational pipeline built on Snakemake to process and analyze bulk RNA sequencing data determine gene expression. It can handle raw from the Gene Expression Omnibus or local FastQ files runs supercomputing cluster. The primary function of align reference genome. To ensure accurate outputs, it also offers trimming, quality control, contaminant screening options. One benefits using that addresses issues commonly encountered with traditional alignment workflows. These include need for manual file naming directory setup, which lead errors problems resuming failed Additionally, these workflows often require many resources requested at once, leading long “wait times” cluster access. Modifying parameters be challenging, as most settings are not localized single file. In contrast, integrates improve resume-ability, minimize resource usage, provide easy parameter modification. Jobs resumed state, only minimum required reduce waiting time, YAML used configure within pipeline. has been four immature natural killer datasets successfully determined expression in samples. capable analyzing RNA-seq input approximately 15 compute minutes, additional do increase runtime due Snakemake’s high interoperability SLURM. removes poor-quality reads downstream analysis presents results an easy-to-read report.