seqclusterViz – visualization of the small RNA transcriptome

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types.

Researchers from the Harvard T.H. Chan school of Public Health and the University of Barcelona describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. The developers demonstrate the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease .

seqclusterViz features


A) Top panel with table showing the list of small RNAs detected (left) and genomic location (right). ( B) Middle panel shows abundance profile over the precursor (left), and secondary structure (right). This is an example of batch effect at the 3’ end (blue higher than brown) and disease effect at the 5’ end (solid lines higher than dashed lines). ( C) Bottom panel shows a table with the top most expressed sequences on the selected small RNA transcript. The index column is the sequence identifier that links the results to the original seqcluster output files.

Pantano L, Pantano F, Marti E, Ho Sui S. (2019) Visualization of the small RNA transcriptome using seqclusterViz. F1000Res.ISCB Comm J-232. [abstract]

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