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].

Victoria and Albert Museum - The Future Starts Here

The Future Starts Here

I found interesting event " The Future Starts Here" in Victoria and Albert Museum, in London. Maybe I am going to visit there soon.

You can feel what's interesting from below URLs.

Victoria and Albert Museum (now until Sunday 4th November, 2018)

https://www.vam.ac.uk/exhibitions/the-future-starts-here

#TheFutureStartsHere hashtag on Twitter

I want to see especially Oxford Nanopore Sequencer MinION, Bento Lab [1] and "Who wants to live forever?".

MinION (UK base) is to do sequencing anywhere by anyone needless to say. Bento Lab (UK base) is to do genetic experience everywhere. When the the mobility is promote, as a result the most popular CPU company for the mobile device, ARM (UK base) is expanded more. The age of personal biology is starting now.

UK government campaign

By the way, Victoria and Albert Museum is collaborating UK base companies including UK company of multi regional company in variety of way, seasonal events and regular exhibitions.

In 2018, UK government is promoting a campaign "The Year of Engineering" [2]. It seems that the government is fighting against the separation of the some global companies by Brexit, and trying to change the country such as Switzerland and Singapore. I saw an article that UK government people visiting Switzerland to observe the strategy on BBC news.

The Year of Engineering is a government campaign which celebrates the world and wonder of engineering.