GISTIC Refgene files

[Andrew Cherniack]

Is there a way to import your own Reference Genome matlab file into Gene Pattern GISTIC?

We are finding that the HG19 refgene file seems to missing some genes that we are interested in.

[tmt...@cloud.ucsd.edu]

Hello,

At the moment we don't have an easy way to use your own refgene file with the GISTIC module. However, that looks like an easy change for us to make. We will aim to release a new version of the module next week that can accept a custom refgene.

Thorin Tabor
GenePattern Team

[Andrew Cherniack]

Thank you!

Best,

Andy

___________________________
Andrew Cherniack, PhD                                               
Senior Group Leader

Cancer Program
Broad Institute of Harvard and MIT
415 Main Street
Cambridge, Mass 02142
email: ache...@broadinstitute.org
___________________________

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[tmt...@cloud.ucsd.edu]

Hello,

A new version of the GISTIC_2.0 module has been released that supports custom refgene files.

Thorin Tabor
GenePattern Team

[Andrew Cherniack]

Hi Thorin,

Thanks for doing this.  I was able to run GISTIC with my own reference gene file.

However, I just found a bug while trying it out for GISTIC 6.15.28.

Remove X in the advanced parameters does not work correctly.  I set the flag to not remove X. 

In Matlab remove X should be set to 0 in this case.

But when I ran GISTIC the X was removed.  

In the Matlab output  remove X was set to 1

I am going to trying it out on the previous version of GISTIC

Regards,

Andy

___________________________
Andrew Cherniack, PhD                                               
Senior Group Leader

Cancer Program
Broad Institute of Harvard and MIT
415 Main Street
Cambridge, Mass 02142
email: ache...@broadinstitute.org
___________________________

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[Andrew Cherniack]

For version 6.15.21.

The remove X parameter works correctly.

Both GenePattern versions use GISTIC  2.0.23. and so GISTIC itself is unlikely to be the issue.

Andy

[tmt...@cloud.ucsd.edu]

Thank you for pointing this out. I'll see if I can reproduce the issue and create a fix.

Thorin Tabor
GenePattern Team

[tmt...@cloud.ucsd.edu]

Hello Andy,

I was able to reproduce your issue and a new version of the GISTIC_2.0 module has been released that fixes the remove.X bug.

Thorin Tabor
GenePattern Team

[Andrew Cherniack]

Thanks again!

Andy

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