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Fig. 4 | Genome Biology

Fig. 4

From: DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Fig. 4

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

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