runChicago.R

[Rola Dali]

Hello,

I am trying to run chicago on my capture hic using the runChicago.R wrapper. I find there is not much documentation regarding the wrapper itself. I keep getting this error:

Normalising baits...
Reading NPerBin file...
Error in .readNPBfile(s = cd@settings) : 
  The minFragLen in the NPerBin file header is not equal to minFragLen defined in experiment settings. Amend either setting (and if needed, generate a new NPerBin file) before running the analysis
Calls: chicagoPipeline ... .normaliseFragmentSets -> setkeyv -> is.data.table -> .readNPBfile
Execution halted

I have tried adding "--minFragLen=0" to the command line of runChicago.R or adding it the chicago_settings file but it doesnt seem to work.

How do I modify the 'minFragLen' variable for the runChicago.R wrapper?

Thank you!

[Mikhail Spivakov]

You will need to create a custom settings file, in which you modify this parameter from the default value, and supply it as an argument to runChicago. I'm not near a computer at the moment but check the docs for the R package on creating this file and if you need more detailed instructions please post back.

[Mikhail Spivakov]

PS. The wrapper docs are in the readme file on bitbucket.

[Rola Dali]

Thanks for the quick reply. It is not obvious to me how to do that and what the format of the settings file is. I would like to get a bit more information once you have the time. Thanks!

[Mikhail Spivakov]

The format is (tab-separated): <Parameter-name> <value>

Then in runChicago.R, you'll need to provide the name of the settings file as --settings-file <filename>.

Hope it helps.

[Rola Dali]

Thank you!