RNA-seq differential expression analysis workflow generally consists of four steps: (i) retrieving data, (ii) quality control (QC), (iii) de novo assembling and/or read mapping, and (iv) statistical analysis. We explain the third step with a recent QC program FaQCs (ver. 1.34). We introduce de novo transcriptome assembly by Rockhopper2 (ver. 2.0.3; a Java program) and mapping for a Lactobacillus genome by QuasR (ver. 1.8.4; an R/Bioconductor program). We demonstrate the importance of QC.

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