IGV interpretation

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Integrated genome browser (IGV) is a high performance visualization tool to interactively explore large-scale integrated genomic data. It supports a variety of data types, and including the next generation of array-based sequencing and gene annotation data. IGV this tool is cattle, made NB:

James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011)

The basic idea of using IGV

Installation and Configuration

IGV on linux use (you first need to go to the official website to download a Linux IGV), then the need for a remote control tool:

Here use VNC, online download crack version , installation (enter the registration code to crack, there is registration code bottom of the article).

Run IGV

After the open VNCserver linux, open, and displays the node and port on linux, Windows terminals for connection.

vncserver -geometry 1366x768 # resolution adjustment

After opening the service, Linux nodes may be prompted to log in, log on VNC need your ip, port and VNC password.

Run VNC client (VNC viewer) in the IGV.sh open visualization program (Open the Windows VNC will automatically jump to the IGV installation directory under Linux, IGV.sh double-click to open).

1. Loading data reference genome

You can click on a selection, you can also load the file menu bar Genomes.

2. bam file after loading the sort

By File menu bar, load from file. . .

Preparation visualization data IGV

What data can not take a look at the IGV, reference genome must be FASTA format;

IGV than just responsible for results visualization, and no comparison process, it is not loaded directly reads;

reads previously specified reference genome need to be aligned for comparison with the BWA;

Sam than the file can not be loaded directly into (trouble), to turn bam; bam sort; bam construction index (can be done one step);

Command process is as follows:

BWA out IGV sam file can not be directly utilized, must in order to be displayed after samtools treatment IGV.

samtools view -@ 10 -bS -F 4 ./contigs_sequence_align_to_public_genome.sam > ./contigs_sequence_align_to_public_genome.bam

samtools sort -@ 10 ./contigs_sequence_align_to_public_genome.bam contigs_sequence_align_to_public_genome.sorted

samtools index contigs_sequence_align_to_public_genome.sorted.bam contigs_sequence_align_to_public_genome.sorted.bai

samtools depth contigs_sequence_align_to_public_genome.sorted.bam >depth_reads.txt

wc -l depth_reads.txt > Coverage-aln_reads.txt

More details with reference to the use of samtools use .

IGV need to set the memory, the memory is eating while watching a large genome.

Example:

Shown below is the assembly anomaly, this is where a manual connection, Pacbio all can not be successfully cross over, assembling problems.

The following are specific to a single cell transcriptome Visualization:

IGV basic operations

How to remove the right of automatic pop-up box?

Blue box reads up is what?

IGV User's Guide

用户界面
开始使用IGV
导航
加载一个基因组
外部控制IGV
查看参考基因组
加载数据和属性
查看数据
查看比对（核心）
查看Variants
基因列表视图
感兴趣的区域
样本的属性
排序、分组和过滤
保存和恢复会话
服务器配置
Motif查找器
igvtools
BLAT 搜索

1.用户界面

1.1 Main Window（主窗口）

1.tool bar（工具栏），menu bar（菜单栏），pop-up menus（弹出式菜单）。

2.染色体上的红色盒子表示显示这部分染色体，显示完整染色体是红框会消失。

3.尺度显示了染色体的可见部分，刻度线显示了染色体的位置，跨度列表显示了当前显示的碱基的数量。

4.IGV在水平行显示的数据称为tracks。通常,每个tracks代表一个样本或实验。这个例子展示了甲基化、基因表达、拷贝数，LOH和突变数据。

5.IGV也显示某些特性,比如在tracks中的基因。默认情况下,IGV在一个面板显示数据，在另一个面板显示数据特性。拖放一个track名称，将一个track从一个面板移动到另一个地方。

6.Track名称列在最左边面板。名字的易读性取决于 tracks的高度，例如，track越小，它的名字的可读性越小。

7.属性名称被列在顶部的属性面板。彩色块代表属性值,每个独特的值被都有一个独特的颜色。鼠标放在一个颜色块的附近来查看其属性值。

参考资料

IGV官网

IGV User Guide 和 HTML版本

Viewing Alignments（查看比对，核心文档）

IGV软件使用指南(博客)

修改VNC分辨率大小

软件安装：

RealVNC是一款免费的远程控制程序，它是VNC （Virtual Network Computing）众多操作平台版本中的一员，这里小编提供的RealVNC适用于windows操作平台，软件采用2048 位 RSA 服务器验证和 128 位 AES 会话加密术，安装此软件的电脑可在全球各地远程操控自己的电脑，所操作平台没有任何限制。

功能特色

1.Windows 验证 —— 允许访问 VNC 服务器以便控制基于标准的 Windows 用户证书，无论其是本地的、NT 域或者基于 Active Directory。
2.单一登录 —— 允许在一个域内部访问 VNC 服务器而不需要重新输入用户的名称和口令。
3.简单但有效的部署 —— 用 VNC Tool，即 VNC Deployment Tool for Windows 安装和管理 VNC Enterprise Edition 服务器。
4.桌面缩放 —— 通过精确的比例缩放，或动态缩放为任何大小。
5.Windows 防火墙集成 —— 使 VNC Server 可以更直接的部署。
6.文件传输 —— 与 Windows 剪贴板结合，允许通过 VNC 连接在服务器和查看器计算机之间复制文件而不需要额外的配置。
最好的就是，与 VNC Enterprise 系列的其他产品一样，VNC Enterprise Edition for Windows是由原始 VNC team 设计、开发和维护的。

RealVNC注册码

3YHED-MNEHC-RMJT5-4UAAK-6A5HA
FBV9V-7Z3V9-MED3U-47SEU-85T3A
HA7MG-J8R3J-R3528-HC6P5-HTQ6A
B7SLM-7MAX5-B4M74-UTDBE-K5WFA
7736G-H4YBP-6ZCEU-AM3H4-QBTWA
NUQQ6-UP89V-9XGPU-GUYU9-U6VTA

The basic idea of ​​using IGV