RNA-seq teaching module using SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis¶
SPARTA is a workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms. The workflow combines several tools: Trimmomatic (read trimming/adapter removal), FastQC (read quality analysis), Bowtie (mapping reads to the reference genome), HTSeq (transcript/gene feature abundance counting), and edgeR (differential gene expression analysis). Within the differential gene expression analysis step, batch effects can be detected and the user is warned of the potential, unintended additional variable. The analysis procedure is outlined below.
However, before we can dive into doing the data analysis with our own data or some example data it is worth having a look at some background information first.
How to get and use SPARTA:¶
Mac Users - Mac OS X tutorial
Windows Users - Windows tutorial
Linux Users - Linux tutorial
Contribute: If you would like to contribute to the project, the source code for each platform can be found in the GitHub repository.