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?