What's the output file in CNAnator

[yuhao]

I see the result produced by CNVnator on the screen, but we need the output file stored somewhere, is there any file ? Another question is what the bin_size I really need to choose? Does that matter the result significantly? I want to detect the CNV in cancer cell of human. I see the default is 100, but someone even choose 1000, I just dont know if it is a very sensitive parameter in terms of the quality of the output result? Thx for help!Thx for help!

[ECO]

Uhhhh redirect stdout to a file?

Command > filename

Just a guess.

[yuhao]

Hi, can you be more specific?What the command is to redirect stdout to a file?Thank you so much !

[david_2012]

Dunno if that is still useful, but here is a more specific answer to what the command is:

ECO actually pointed it out. In any linux shell (e.g. bash), which is just the linux command line, the sign to use when you want to redirect standard output of a command to a file instead of the terminal window is ">". So on the command line you type:
"any command" > "any filename"

In CNVnator this at least works for the CNV CALLING step. E.g. with a bin size of 80 this would be:
cnvnator -root file.root -call bin_size 80 > results.cnv

And you find your results in a file called "results.cnv" in the directory that you ran the command in.