IGV-Introduction_igv cds intron-优快云博客

title	author	date
Basic IGV Introduction	Banner Wang C	November 11th, 2021

Learning Objectives

https://github.com/griffithlab/rnaseq_tutorial/wiki/IGV-Tutorial

1	The tool bar provides access to commonly used functions. The menu bar and pop-up menus (not shown) provide access to all other functions.
2	The red box on the chromosome ideogram indicates which portion of the chromosome is displayed. When zoomed out to display the full chromosome, the red box disappears from the ideogram.
3	The ruler reflects the visible portion of the chromosome. The tick marks indicate chromosome locations. The span lists the number of bases currently displayed.
4	IGV displays data in horizontal rows called tracks. Typically, each track represents one sample or experiment. This example shows segmented copy number data.
5	IGV also displays features, such as genes, in tracks. By default, IGV displays data in one panel and features in another, as shown here. Drag-and-drop a track name to move a track from one panel to another. Combine data and feature panels by selecting the option to display all tracks in a single panel on the General tab of the Preferences window.
6	Track names are listed in the far left panel. Legibility of the names depends on the height of the tracks; i.e., the smaller the track the less legible the name.
7	An optional attribute panel displays sample/track attributes represented as colored blocks, where each unique value is assigned a unique color.

请添加图片描述

Sequence top base：A(green)，C(blue)，G(orange)，T(red)，repeat sequence will be more remarkable.
Amino acids are displayed as blocks colored in alternating shades of gray. Methionines蛋氨酸 are colored green, and all stop codons are colored red. When you zoom all the way in, the amino acid symbols will appear.
Click the first row of ac, it will disappear.
You can change the strand that is displayed by clicking on the arrow in the title to the left of the track. Note that the sequence and the arrow are only displayed when zoomed in to a sufficiently small region.
The direction of the arrow indicates which strand is currently displayed. An arrow pointing left indicates that the negative strand is showing. This strand will show the complement nucleotides and reverse complement translations.

Load gtf file,it should be sorted and indexed, in Tools/Run igvtools.
Display overlapping features, such as different transcripts of a gene, on one line or multiple lines
Vertical bars represent exons. The taller bars are CDS within the exons (thus, the shorter vertical bars are UTR). Arrows are the 5'->3' direction (so if they pointed in the other direction, the gene would be on the - strand).
exon and intron connected by conserved sequence. GT-AG principle[RNA splicing signal] : Tail of exon to head of intron [GT]，tail of intron to head of exon.
Region label : Regions - Region Navigator