Jun's Blog

Output, activities, memo and etc.

Mark Zuckerberg's Speech at Harvard

Others

news.harvard.edu

My favorite parts in the speech.

"I’ve sat with children in juvenile detention and opioid addicts, who told me their lives could have turned out differently if they just had something to do, an after school program or somewhere to go."

"We can all make time to give someone a hand. Let’s give everyone the freedom to pursue their purpose — not only because it’s the right thing to do, but because when more people can turn their dreams into something great, we’re all better for it."

"The greatest successes come from having the freedom to fail."

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

Bio-tech

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].