Question

How to use igv on ubuntu

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6.5 years ago

mikysyc2016 ▴ 120

After peakcalling, i want to use igv to see my data(bedgraph). But i can not install IGV. Do you have good suggestion? Thanks!

ChIP-Seq • 23k views

ADD COMMENT • link updated 6.5 years ago by Arup Ghosh 3.2k • written 6.5 years ago by mikysyc2016 ▴ 120

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But i can not install IGV.

Please elaborate on what you tried and what didn't work.

ADD REPLY • link 6.5 years ago by WouterDeCoster 47k

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6.5 years ago

Arup Ghosh 3.2k

Download and unzip IGV binary distribution file. Then navigate to IGV_2.4.10 and modify igv.sh and modify the amount of RAM -Xmx20g (change 20) and open a terminal on the same folder to run ./igv.sh.

ADD COMMENT • link 6.5 years ago by Arup Ghosh 3.2k

score 7 · Accepted Answer · 2018-06-12

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6.5 years ago

JC 13k

If you are using Ubuntu 18.04 you can do sudo apt install igv

For previous versions you need something like:

sudo apt install default-jre
curl -LO http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.10.zip
unzip IGV_2.4.10.zip
cd IGV_2.4.10
sudo ln -s $PWD/igv.sh /usr/local/bin/
igv.sh&

ADD COMMENT • link 6.5 years ago by JC 13k

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"If you are using Ubuntu 18.04 you can do sudo apt install igv". I install it, but do not how to open it and use.

ADD REPLY • link 6.5 years ago by mikysyc2016 ▴ 120

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open a terminal and type igv

ADD REPLY • link 6.5 years ago by JC 13k