How to Setup JBrowse in Ubuntu?

How to Setup JBrowse in Ubuntu?

1. Install build prerequisites, plus make and a C compiler. On Ubuntu, you could do this with below command.

sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential

2. Download JBrowse zip file (JBrowse-1.10.12.zip) from http://jbrowse.org/jbrowse-1-11-0/

3. Place the downloaded zip file in /var/www/JBrowse.

4. Unzip the zip file (JBrowse-1.10.12.zip) using the following command.

unzip /var/www/JBrowse/ JBrowse-1.10.12.zip

5. Allow read write access to /var/www/JBrowse folder using the following command.

sudo chown ‘user’ /var/www/JBrowse

6. Make sure you are installed with GD, Libpng & Curl libraries.

7. Run the following command.

sudo apt-get install libpng12-0 libpng12-dev build-essential libcurses5-dev

8. Go inside /var/www/JBrowse/JBrowse-1.10.12/, run ./setup.sh

9. Now you are ready to access JBrowse in your machine. Open internet explorer & type the following url http://localhost/JBrowse/JBrowse-1.10.12/index.htm

What other tools needed for Jbrowse?

Yes the following tools are needed.

bgzip & tabix

  • Compress your .vcf file using the bgzip program

bgzip my.vcf

  • For more information about the bgzip command, run bgzip with no other arguments.
  • Create a tabix index file for the bgzip-compressed VCF (.vcf.gz)

tabix -p vcf my.vcf.gz

The tabix command appends .tbi to my.vcf.gz, creating a binary index file my.vcf.gz.tbi with which genomic coordinates can quickly be translated into file offsets in my.vcf.gz.

  • Move both the compressed VCF file and tabix index file (my.vcf.gz and my.vcf.gz.tbi) to an http, https, or ftp location.

For more info, please refer – http://genome.ucsc.edu/goldenPath/help/vcf.htm

Samtools

  • Sort and create an index for the BAM

samtools sort my.bam my.sorted

samtools index my.sorted.bam

The sort command appends .bam to my.sorted, creating a BAM file of alignments ordered by leftmost position on the reference assembly. The index command generates a new file, my.sorted.bam.bai, with which genomic coordinates can quickly be translated into file offsets in my.sorted.bam.

  • Move both the BAM file and index file (my.sorted.bam and my.sorted.bam.bai) to an http, https, or ftp location.

For more info, please refer – http://genome.ucsc.edu/goldenPath/help/bam.htm