Fig. 1From: SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome AnalysisSPARTA workflow diagram. Single-end Illumina FASTQ files, a FASTA formatted reference genome, and genome feature file (gff or gtf) are given as inputs to the workflow. Trimmomatic and FastQC perform trimming of adapters and low quality bases/reads and quality assessment reports, respectively. Bowtie maps the trimmed reads to the reference. HTSeq quantifies transcript abundance. R/edgeR tests for statistically significant genes and warns the user of potential batch effects present in the analyzed data setBack to article page