SPARTA (Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis), is a tool for transcriptomic analysis of bacterial Illumina RNA-seq data. SPARTA can analyze single-end data. The Pipeline includes FastQC, Bowtie, HTSeq, edgeR, and output consists of QC reports, gene feature counts, differential gene expression, and scatterplots.
Transcriptomics; RNA-seq
Johnson BK, Scholz MB, Teal TK, Abramovitch RB "SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis." BMC Bioinformatics. 2016 Feb 4;17:66. https://doi.org/10.1186/s12859-016-0923-y
PMID: 26847232
PMCID: PMC4743240
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