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IGV and IGVTools
IGV logo

Description

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. Features include:

Interactive Use

This application requires an X-Windows connection.

IGV uses environment modules. Type

module load igv

at the prompt. Then type

igv

NOTE: When running on Biowulf, make sure that web proxying is enabled by first typing the command proxyon. Otherwise you may get a java error message about being unable to connect to remote hosts. For information about web proxies on the Biowulf cluster, see here.

Environment variables set:

Here are the commandline options:

The igv command on Helix is wrapped to include two additional options:

By default, IGV uses 1gb of memory and uses either /lscratch/$SLURM_JOBID/igvtmp if --gres=lscratch:N is used in a batch job (where N is the number GB needed for scratch space, or /scratch/$USER/igvtmp as the temporary directory, where $USER is the login of the user running IGV. To allocate 20gb of memory, use:

igv --memory 20g

Input/output for IGV is menu-driven through the GUI:

IGV display window

IGVTools

IGVTools allows commandline utilities for working with ascii file formats.

To use IGVTools, type

module load igvtools

at the prompt. Then type

igvtools

IGVTools is also available as a GUI. Type

igvtools_gui

at the prompt.

Environment variables set:

By default, IGVTools uses 5gb of memory and the same temporary directory method as IGV. To allocate 20gb of memory, use:

igvtools --memory 20g [ additional options for igvtools ]

To see what options are available for the commandline IGVTools, just type igvtools at the prompt:

Program: igvtools. IGV Version 2.2.2 (5)03/06/2013 06:46 PM

Usage: igvtools [command] [options] [input file/dir] [other arguments]

Command: version print the version number
         sort    sort an alignment file by start position. 
         index   index an alignment file
         toTDF    convert an input file (cn, gct, wig) to tiled data format (tdf)
         count   compute coverage density for an alignment file
         formatexp  center, scale, and log2 normalize an expression file
         gui      Start the gui
         help      display this help message, or help on a specific command
         See http://www.broadinstitute.org/software/igv/igvtools_commandline for more detailed help

Documentation