RNASeqBrowser: a genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

BMC Genomics
Jiyuan AnColleen C Nelson

Abstract

Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets. This paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. Finally, RNASeqBrowser was designed for ease of use for users with few bioinformatic skills, and incorporates the features of many genom...Continue Reading

References

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Citations

Nov 28, 2017·Clinical Epigenetics·Lu GaoCarrie V Breton
Feb 18, 2016·European Journal of Human Genetics : EJHG·Katie M O'BrienClarice R Weinberg
Jun 29, 2018·Genome Biology·Sidney H WangJonathan K Pritchard
Feb 6, 2018·European Journal of Human Genetics : EJHG·Laura AndreasenJesper H Svendsen
Jul 25, 2019·Genes, Chromosomes & Cancer·Karin WallanderKristina Lagerstedt-Robinson
May 27, 2016·Journal of Experimental & Clinical Cancer Research : CR·Samantha KaufholdBenjamin Bonavida
Jan 17, 2019·Annals of the New York Academy of Sciences·George R Uhl, Maria J Martinez
Feb 17, 2017·BMC Genomics·Hechuan YangYaping Zhang
Jun 13, 2020·Circulation Research·Wilson Lek Wen TanUNKNOWN CHARGE-Heart Failure Working Group, CHARGE-EchoGen Consortium
Apr 1, 2016·Chronobiology International·M SotákA Sumová
Mar 21, 2019·Cancer Informatics·Zhonglin QuDaniel R Catchpoole
Apr 9, 2015·Journal of Thrombosis and Haemostasis : JTH·A C Goodeve

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Methods Mentioned

BETA
ChIP-Seq
pull down
pull-down
RNAseq

Software Mentioned

savant
Ucsc genome browser
RNASeqBrowser
Tablet genome browser
ZENBU
genomeView
Ensembl
IGV
VarScan
Tablet

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