How do I run IGV on Linux?

Table of Contents

Download and unzip the binary distribution archive in a folder of your choosing. IGV is launched from a command prompt — follow the instructions in the readme file. To launch IGV on Mac or Linux use the shell script igv.sh. On Windows use igv.

How do I run IGV on a server?

4 Answers

Download and install IGV for linux from the IGV site on to your server.
Connect to the server using ssh with X11 forwarding enabled. ssh -X user@server.
Navigate to the recently downloaded and unzipped IGV folder. Execute the igv.sh script. ./igv.sh.

What is IGV tool?

The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. It supports flexible integration of all the common types of genomic data and metadata, investigator-generated or publicly available, loaded from local or cloud sources.

How do I run IGV in Ubuntu?

How To Install igv on Ubuntu 20.04

sudo apt-get update. Copy. After updating apt database, We can install igv using apt-get by running the following command:
sudo apt update. Copy.
sudo aptitude update. Copy.
sudo apt-get -y purge igv. Copy.

How do I allocate more RAM to IGV?

First edit the igv. command file to increase the max memory in the -Xmx Java option. You can also set a lower starting memory by adding the -Xms options.

How do I read IGV data?

Hover over or click a read to view information about the read, including the location of its paired mate. IGV colors (1) paired end reads with inferred insert size smaller or larger than expected; (2) read with mate that is aligned to a different chromosome; (3) paired-end alignments with deviant pair orientation.

How do I view BAM files in IGV?

In IGV, select File > Load from URL … A window will pop up and ask you to give the correct URL for the file you want to view. Paste in the URL and the file will be downloaded. From the file extension, IGV will automatically treat the information in the file accordingly.

How do you use IGV BAM?

How to start IGV on Linux?

Alternatively, you can start IGV with the script igv.sh inside the IGV_Linux_2.5.0 directory. You might have to make the script executable first by typing:

How do I create a directory called “IgV”?

We’ll first create a directory called “igv” in your home directory. You can determine your home directory by issuing the following command in a Terminal window on Linux or Mac: echo $HOME On Windows, open a command window by clicking Start, then Run, then typing cmdand pressing Enter.

How do I import a gene file into IgV?

Enter the ID and Name of the Genome you are working with (these can be anything that makes sense to you) and select the path to your *.fasta file (the index, *.fai file needs to be in the same directory), then select the path to your *.gff file for the Gene File. From the main window of IGV, click on File? Load from File….

How do I run igvtools from the command-line?

Once the GUI version has been launched, the commands and options are the same as when you run igvtools from the IGV interface. The general form of the command-line version is: igvtools [command] [options] [arguments] — or– igvtools.bat [command] [options] [arguments]