Katz Yarden, Wang Eric T, Silterra Jacob, Schwartz Schraga, Wong Bang, Thorvaldsdóttir Helga, Robinson James T, Mesirov Jill P, Airoldi Edoardo M, Burge Christopher B
Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, Department of Biology, MIT, Cambridge, MA.
Department of Biology, MIT, Cambridge, MA.
Bioinformatics. 2015 Jul 15;31(14):2400-2. doi: 10.1093/bioinformatics/btv034. Epub 2015 Jan 22.
Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples.
To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.
Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html
RNA测序（RNA-Seq）数据分析表明，绝大多数人类基因表达多种mRNA异构体，这些异构体由前体mRNA可变剪接和其他机制产生，并且大多数可变异构体在人体组织间的表达存在差异。随着RNA-Seq数据集规模的不断扩大，跨多个样本可视化异构体表达仍然具有挑战性。
为帮助解决这一问题，我们展示了生鱼片图，这是一种对比对后的RNA-Seq reads进行定量可视化的方法，能够对跨样本或实验条件下的外显子使用情况进行定量比较。生鱼片图可以使用Broad综合基因组浏览器或独立的命令行程序生成。
软件代码和文档可在此处免费获取：http://miso.readthedocs.org/en/fastmiso/sashimi.html
