Advice on Cytoscape heat diffusion network analysis for CRISPR/cas9. Currently >3hrs run time.

[AliH]

Hi,

I am new to cytoscape, looking for advice on running a CRISPR cas 9 network analysis. I have analysed my data to create a list of significant genes, but now I want to arrange these genes into biological pathways.

I am using cytoscape recipe ‘identify essential genes and associated networks from CRISPR/cas9 genome wide screen’ using the protocol http://recipes.genomespace.org/view/75#collapse_5.

I have downloaded the NDex network, uploaded my gene table and selected for only significant genes (about 200 nodes) and run ‘diffuse selected nodes’

The analysis appears to be running, but current run time is over 3hrs, and using around 60% computer memory.
This is the second time I have tried to run, I aborted the first run after 4hrs. The second run is on my home WiFi, previously tried work WiFi.

Can anyone offer any advice on this issue.

Many thanks,

AliH

[Dexter Pratt]

Can you share your table of 200 significant genes so we can reproduce the behavior?

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[Alison Howarth]

Hi,

Thank you for getting back to me, I was able to resolve the issue by moving to a cabled computer with better processing.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/BLUPR01MB1236E86E399D652E35D58907F0EF0%40BLUPR01MB1236.prod.exchangelabs.com.