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bedtools BED to IGV (version 2.30.0)

Create IGV batch script for this BED/bedGraph/GFF/VCF/EncodePeak file:

Sort BAM file by:

The type of BAM sorting you would like to apply to each image.

Collapse the aligned reads prior to taking a snapshot?:

Use the name field (column 4) for each image's filename.:

Default is to use chr:start-pos.

Number of flanking base pairs on the left and right of the image.:

Select the type of image to be created.:

What it does

Creates a batch script to create IGV images at each interval defined in a BED/bedGraph/GFF/VCF/EncodePeak file.

Notes

The resulting script is meant to be run from within IGV.
It is assumed that prior to running the script, you've loaded the proper genome and tracks.

This tool is part of the bedtools package from the Quinlan laboratory.

Citation

If you use this tool in Galaxy, please cite:

Bjoern A. Gruening (2014), Galaxy wrapper