Sashimi plots do not work

[Christy Susan Varghese]

Hello all,

Good morning.

I have installed IGV for Windows (Java included). 

My Sashimi plots work only sometimes. Why is this so?

Many thanks for your help.

Best regards,

Christy

[Helga Thorvaldsdottir]

Hi Chisty,

What do you mean that it only works sometimes? Please provide more detail so we can try to reproduce the problem. For example, can you describe the steps of what you are doing, and how it fails. Do you see any error messages in the igv.log (found in the igv folder in your home folder)? Often screenshots/screencasts will help, if it's hard to describe.

Helga

[Helga Thorvaldsdottir]

Hi Christy,

From the screenshot you sent, it looks like you do not have any gene annotation tracks loaded. To create the Sashimi Plot, IGV needs as input a track that contains the transcript annotations. It can be a track that you load into IGV specifically for that purpose, or it can be the gene annotation track for the reference genome that is loaded. For the IGV-hosted genomes, a default gene annotation track is always loaded by default, but since you are using your own, you will also need to load a track that has transcript annotations for your genome, or at least for the region you are interested in.

Helga

[Christy Susan Varghese]

Hello Helga,

Thank you for your email.

So I uploaded the annotation file -> and I am trying Sashimi plot -> I am getting the green circled window (attached) -> not the nice colored histogram

Could you explain why?

Thank you very much.

Best regards,

Christy

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[Helga Thorvaldsdottir]

Hi Christy, 

Did you delete the alignment track? Try it again with the alignments there. Note, if you don't want to see the alignments, you can hide them by right-clicking and unselecting "Show Alignment Track" - that won't affect the Sashimi Plot.

Helga