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
- Create a sorted bam file from the bam file created previously.
- Then create an index file from the sorted bam file.
- 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.
I referred Japanese Tutorial [3], [4].