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. 2016 Feb 4;17:66. doi: 10.1186/s12859-016-0923-y

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© Johnson et al. 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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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