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Fig. 1 | BMC Bioinformatics

Fig. 1

From: SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis

Fig. 1

SPARTA 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 set

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