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This article shows you how to use igvtools to visualize the depth distribution of sequencing. The content is concise and easy to understand, and it will definitely brighten your eyes. I hope you can get something through the detailed introduction of this article.

Igvtools is one of the most commonly used NGS data visualization tools. It is very powerful and can show the distribution of many kinds of data, such as sequence alignment, copy number variation, mutation site, etc.

The editor mainly introduces how to use this tool to show the distribution of sequencing depth. For sequencing depth, there are files in a variety of formats that store the corresponding information, such as bedgraph, bigwig and so on. Igvtools certainly supports direct import of files in this format, but igvtools officials prefer to use one of their own file formats-TDF.

The TDF format also uses a sliding window to represent the results of the window with the average of the data in the window, resulting in a binary file that is faster to process with igvtools. Through the command line tool of igvtools, you can generate the corresponding tdf format file from the bam file, using the following

Igvtools count\

-z 5-w 10-e 0\

Sample.bam\

Sample.tdf\

Genome.fa

Once the file in tdf format is generated, you can import it into igvtool, select the corresponding genome version first, and then import the corresponding file through File- > Load from File.

In order to make the display more beautiful, we make some adjustments to the default parameters. Through the View- > Preferences button, adjust the parameters of Charts, and check the corresponding radio box, as shown below

In igvtools, the data displayed in each row is called track, and the color and value range of each track can be adjusted through the right-click pop-up menu. After adjusting the parameters, you can produce the results shown below

Igvtools also supports the export of pictures, through File- > Save Images can export png, svg, jpeg and other formats of files.

The above content is how to use igvtools to visualize the sequencing depth distribution. Have you learned the knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

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