This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tool: StarScan: scanning small RNA targets in lncRNA, circRNA, mRNA and pseudo genes from degradome sequencing data

StarScan (small RNA target Scan) is the first web-based software for discovering potential sRNA-mediated RNA cleavage events from degradome sequencing data in plants and animals (20 species). StarScan searches small RNA (miRNA, siRNA, piRNA, etc.) targets in annotated (lncRNAs, circRNAs, pseudogenes, 5' UTR, CDS, 3' UTR and introns) and unannotated genomic regions. StarScan web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in various genomic regions.

Please visit StarScan website or read our StarScan paper (Nucleic Acids Res. 2015 May 18. doi: 10.1093/nar/gkv524) for details.

StarScan scan sRNA targets using 100 degradome sequencing datasets from 20 species.

circrna rna-seq mirna lncrna degradome-sequencing
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updated by Ram Ram • written by lsp03yjh lsp03yjh

1 answer

We developed a novel StarScan Browser to provide an integrated view of reference sequences, genes, transcripts and cleavage locations refer to genome coordinates. All cleavage location annotations were curated by StarScan web server.StarScan Browser is built on JBrowse, which is a fast, smooth scrolling and zooming genome browser.

Features:

  1. Displays cleavage locations from each degradome sequencing data sample integrated by StarScan.
  2. Displays cleavage locations from each sample in separate strands.
  3. Displays cleavage abundance in RPM values.

starScan Browser

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updated by Ram Ram • written by lsp03yjh lsp03yjh

Awesome jbrowse :)

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written by cmdcolin cmdcolin

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