```{r setup，echo = false} stopifnot（Biocinstaller :: biocversion（）==“3.0”）`````{R样式，Echo = False，结果='Asis'} Biocstyle :: Markdown（）```##附录1：安装和使用igv _note_：应在笔记本电脑上执行此文档中的所有说明，而不是在Rstudio服务器AMI上执行**。*我们首先在主目录中创建一个名为“igv”的目录。您可以通过在Linux或Mac上的终端窗口中发出以下命令来确定您的主目录：echo $ home在Windows上，通过单击“开始”打开命令窗口，然后运行，然后键入`cmd`并按Enter键。在窗口中，键入echo％userprofile％*所以转到指示的目录，然后发出命令mkdir igv，它将在主目录中创建一个`igv`目录。*将文件[hg19_alias.tab]（hg19_alias.tab）复制到此目录。这是一个简单的标签分隔文件，它在对齐方式使用的序列名称之间映射，以及IGV已知的序列名称。*如果您还没有，请安装Java。转到[https://www.java.com/en/](https：//www.java.com/en/），然后单击免费java下载。下载并安装。 * Download IGV from [https://www.broadinstitute.org/igv/download](https://www.broadinstitute.org/igv/download). There are several ways to do this, the easiest is to click on one of the Java Web Start links. Make sure you have more memory available than what is listed below the Launch button. You may need to change the security settings on your computer to allow IGV to launch. * With IGV running, let's change the default genome. It's currently set to Human hg18, so click on the dropdown in the upper left that says "Human hg18". Click on "More..." and then in the `Filter` box, start typing `hg19`. `Human hg19` will then show up in the box and you can double-click on it. We're now using Human hg19 as our default genome. * You can now open bam files in IGV. Here are the URLs of BAM files for this class. You can open them by clicking on IGV's `File` menu, then clicking on `Load From URL...`. You can paste one of these URLs into the box and click OK:http://s3-us-west-2.amazonaws.com/oct2014bamfiles/srr1039508_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/srr1039509_sorted.bam http：// s3-us-West-2.Azonaws.com/oct2014bamfiles/srr1039512_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/srr1039513_sorted.bam http://s3-us-west-2.amazonaws.com/Oct2014Bamfiles / srr1039516_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/srr1039517_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/srr1039520_sorted.bam http：//s3-us-west-2.amazonaws.com/oct2014bamfiles/srr1039521_sorted.bam.
您可能会看到一个警告，BAM文件不包含与当前基因组匹配的任何序列名称。您可以忽略此（单击确定）。*通过在框中进入浏览器窗口的顶部中心，通过在框中进入框中的基因符号来放大特定基因，例如sparcl1。然后点击“go`。调整缩放直到读取进入查看，并解释结果。