Fig. 4
From: DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
The DE-kupl pipeline for the discovery and analysis of differentially expressed k-mers. First, Jellyfish is applied to count k-mers in all libraries. k-mers counts are then joined into a count matrix and filtered for low recurrence and matching to the reference transcriptome. Normalization factors are computed from raw k-mer counts and the differential expression procedure is applied. Finally, overlapping differentially expressed k-mers are extended into contigs and annotated based on their alignment to the reference and overlap with annotated genes