runChicago.R

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Issue #17 resolved
Rola Dali created an issue

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!

Comments (6)

  1. 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.

  2. Rola Dali reporter

    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!

  3. 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.

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