Another Japan in the World

Jun Aruga's blog.

Sequencing: view mapped genome on IGV (Integrative Genomics Viewer)

Install Integrative Genomics Viewer (IGV) [1] to view mapped genome. Use bam file that was created previously. See the blog page.

java is used. Install it if it is not installed.

$ java -version
java version "1.8.0_25"
Java(TM) SE Runtime Environment (build 1.8.0_25-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.25-b02, mixed mode)

Install IGV latest version is 2.4.10 on Mac.

$ wget http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.10.app.zip

$ unzip IGV_2.4.10.app.zip

$ mv IGV_2.4.10.app /Applications/

Check supported file formats [2]. .sam and .bam file are supported. The steps are

  1. Create a sorted bam file from the bam file created previously.
  2. Then create an index file from the sorted bam file.
  3. Finally Open the sorted bam file.

Create sorted bam file.

Select Tools -> Run igvtools from menu.

Command: Sort
Input file: SRR747784.bam (Select the bam file created previously).
Output file: SRR747784.sorted.bam

Click "Run".

Create sorted bam file.

Select Tools -> Run igvtools from menu.

Command: Index
Input file: SRR747784.sorted.bam

The index file: SRR747784.sorted.bam.bai is created in a same directory with SRR747784.sorted.bam

View sorted bam file.

Select View -> Load from File. Select the SRR747784.sorted.bam

Now the bam file are displayed in the page.

f:id:happybirthday:20180608072218p:plain

I referred Japanese Tutorial [3], [4].