Essential skills! Cloud Preface teaches you how to easily visualize your genome with IGV

2. After downloading IGV_2.3.59.zip (or any other version), first extract the file and double-click "igv.bat". Run IGV on your own computer (windows system). It takes a while to initialize the IGV (link to the web, download some genomic annotation files).

Second, the operation steps

Part of the reference genomics information is already included in the IGV software storage. You can select it in box 1. If there is a target genome that can be directly clicked, the system will automatically download and import; if not, you can select Genomes→Load Genomes From Files are imported into the local ge file fa file.

Figure 1. IGV interface

2. Introduction of sequencing data

Take the bam or bw file type as an example. Import path: File→Load form File, select bam or bw file; note that bam must be sorted, and there must be a bam file corresponding to the bam file in the directory where the bam file is located. .

Bam file sorting: samtools, sort, A.bam, A.sort

Bam file build index: samtools index A.sort.bam

After importing, you can select the chromosome of interest at the position of box 2 , or you can enter the genomic location of interest at the position of box 3 (format: chromosome: start position - end position ), click Enter to display The coverage of the read of the selected area (the area shown in boxes 4, 5 ). If the selected genome is too large, Zoom in to see coverage will appear in the read coverage area. You can adjust the displayed area by clicking the "+" or "-" in box 6 . If you want to select a gene for visualization, you can type the location of the gene in box 3 , or use Regions→Gene Lists to select the gene set of interest, and of course you can import the list of genes you are interested in.

Figure 2. IGV results show

Also shown in the figure, box 4 is the Coverage track, which indicates the coverage of the sample on the genome, the abscissa is the genomic position, and the ordinate is the sequencing depth at that position. Box 5 corresponds to the sample aligned to the read track on the reference genome, each of which represents a read, which can be displayed by moving the mouse cursor to the read position, and can display the comparison details, and can also visually see each What is the base. When importing bw files, only the content of box 4 is the depth of read coverage, so you want to use the bam file to see the read information.

3. Visualization adjustment

In the actual operation process, it is often necessary to adjust the various additional effects to beautify the picture or meet the requirements of the target magazine. Then move the mouse cursor to the depth area or the read coverage area and right click, a pop-up menu will pop up, corresponding to The function is as follows:

4. Save the picture

When you get your own aesthetic requirements through various parameter adjustments, you can save the picture, right click and select the Save image... function. Of course, in the later stage, we can further adjust it through PS and other beauty software to achieve the icing on the cake!

Today's technology sharing is here, and you are also harvesting a lot like Xiaobian! If you want to dig deeper into the information about the use of IGV, you can also learn directly through the IGV official website!

Official link:

Http://software.broadinstitute.org/software/igv/userguide

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