Fig. 1

Possible bioinformatics pipe-line for RNA-Seq differential expression analysis. The analysis starts with several FASTQ files, produced by the sequencing of several replicates of two conditions (e.g. wild type vs mutant). When a genome is available, the reads are mapped, e.g. with STAR [15], and the corresponding positions are stored into a BAM file. A quantification tool, such as mmquant, presented here, counts the number of reads per gene. Statistical test for differential expression is performed by a third tool, like DESeq2 [6]