Using FunSeq2 for Coding and Non‐Coding Variant Annotation and Prioritization. Issue 1 (2nd May 2017)

• Record Type: Journal Article
• Authors: Dhingra, Priyanka; Fu, Yao; Gerstein, Mark; Khurana, Ekta
• Editors: Bateman, Alex; Pearson, William R.; Stein, Lincoln D.; Stormo, Gary D.; Yates, John R.
• Is Part Of: Current protocols in bioinformatics. Volume 57:Issue 1(2017)
• Page Start: 15.11.1
• Page End: 15.11.17
• Publication Date: 2017-05-02
• Subjects: disease‐causing -- differential gene expression -- cancer drivers -- indels -- non‐coding variants -- single nucleotide variants; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.23
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: The identification of non‐coding drivers remains a challenge and bottleneck for the use of whole‐genome sequencing in the clinic. FunSeq2 is a computational tool for annotation and prioritization of somatic mutations in coding and non‐coding regions. It integrates a data context made from large‐scale genomic datasets and uses a high‐throughput variant prioritization pipeline. This unit provides guidelines for installing and running FunSeq2 to (a) annotate and prioritize variants, (b) incorporate user‐defined annotations, and (c) detect differential gene expression. © 2017 by John Wiley & Sons, Inc.