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Lorena Pantano, Francisco Pantano, Eulalia Marti, Shannan Ho Sui (1 Harvard T.H. Chan School of Public Health, Boston)
The study of small RNA helps us understand part of the complexity of gene regulation of a cell. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. The advantage of small RNA-seq analysis is that we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz (https://github.com/lpantano/seqclusterViz), an interactive HTML-javascript web-page for visualizing small non-coding RNAs (sRNAs) predicted by Seqcluster. Seqcluster is a genome-wide sRNA characterization tool that detects units of transcripts (clusters) using a heuristic iterative algorithm to deal with multi-mapped events. SeqclusterViz is divided into three panels: i) query-ready tables showing 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. It runs locally in the computer making it portable. Seqcluster and SeqclusterViz are integrated into bcbio-nextgen (https://bcbio-nextgen.readthedocs.io/), a community-based python framework.