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Gene network analysis

Hello everyone

I am using cytoscape tool to analyse my RNA-seq data, I am using Kddn app. I have issue when I upload the condition #1 and condition#2 to run Kddn, it takes fore ever and did not come with the final screen to show the data. Does anyone have experience with this issue?

I really appreciate your time and help

Shaima

rna-seq
• 1,545 views • link
updated by Ram Ram • written by saj98 saj98

Hi Shaima, I don't have direct experience with this software but to help you, others will need at least the following additional info:

  • what is the dimension of your data, size of your expression matrix
  • are you only comparing two conditions at a time? do you have replicates
  • forever is not exactly a precise category, so how long did you wait, how much memory did the process use? Maybe you can try it on a subset of the data, say 10% to estimate the timing.
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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

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