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10 changes: 1 addition & 9 deletions docs/source/sashimi.rst
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Expand Up @@ -287,15 +287,7 @@ Command-line options
Making Sashimi plots from IGV
=============================

To create Sashimi plot within IGV, download the snapshot release of IGV:

`IGV Browser snapshot (http://www.broadinstitute.org/igv/projects/downloads/snapshot/IGV_snapshot.zip) <http://www.broadinstitute.org/igv/projects/downloads/snapshot/IGV_snapshot.zip>`_

Run IGV with the Sashimi plot feature enabled: ::

java -jar -Xmx2g -DenableSashimi="true" igv.jar

Load the RNA-Seq samples as BAM tracks. Navigate to the region of interest, right click the tracks window and select "Sashimi plot" from the menu. A customizable Sashimi plot will appear in a new window, which can be saved in PNG or SVG formats.
To create Sashimi plot within IGV [https://software.broadinstitute.org/software/igv/download](http://software.broadinstitute.org/software/igv/download) first load the RNA-Seq samples as BAM tracks. Navigate to the region of interest, right click the tracks window and select "Sashimi plot" from the menu. A customizable Sashimi plot will appear in a new window, which can be saved in PNG or SVG formats.


Visualizing and plotting MISO output
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