How To Set The Proper Parameters When Using Hotnet Web Server?

Question

[Liye Zhang]

Hi, I wonder whether anyone has experience with HotNet, http://ccmbweb.ccv.brown.edu/hotnet/

I tried to use its online (web) version, but I have several questions regarding to the input for the program, can someone help me with it? Thanks a lot. I want to ask few simple questions about running Hotnet on the server. Let's say, I am studying lung cancer, and I have 10 samples. I know what to put for the mutations_file, CNA_file for the length files

Question 1: we just provide the length of the mature mRNA, right?

Question 2: What do I provide for the tested_file in here? Should I provide the genes known to be related to lung cancer? or what?

Question 3: what should I put into the BMR field, if I use the background mutation rate is 4 per Mb?

Question 4: do you have a suggested delta to start with?

Question 5: if I want to run the program to find the threshold, what num_rep and num_threshold do you suggest?

Question 6: what num_rep do you suggest to use if I am running the Hotnet?

Best, Liye

[Istvan Albert]

that's quite a few questions in one post - my best advice would be to find the authors' email then contact them with the request help via email feature above

[Liye Zhang]

I definitely agree with you, I sent them email twice, still no response yet... That is why I am trying to get help from the community.

Answer 1

[Chris Miller]

There seem to be example files here - I'd suggest using them to determine the correct input format: http://ccmbweb.ccv.brown.edu/hotnet/files/HotNet/example/

Alternately, download the package and look at the enclosed README, which doesn't seem to be on their server. It appears to have useful information about formats. http://ccmbweb.ccv.brown.edu/hotnet/files/HotNet_v0.9.1.zip

[Liye Zhang]

Thanks for yout help and comments. Yes, I have looked carefully through the example files and README you pointed out before I post the questions. However, I am still not clear about the parameters I mentioned before. In fact, the some file format requirement(copy number alteration ones) for the local version and web version are different, which confuses me even more.