--en-feat-list

[Stephan Christel]

Hi again,

I have finally successfully created the designDir files, but now had to realize that I still need more input files, including a “feature list file”, to run runChicago.R

The documentation states

en-feat-list: the name of the feature list file of the format <feature-name> <feature-bed-file-location>, where feature-bed-files contain the genomic coordinates of the features to compute the enrichment at Chicago significant interactions
(Chicago signal cutoff 5 is used by default).

I have no idea what that means. I didn't read anything about a feature list before this point (including in the 'Input files required' section of the workflow). How do I get this file, i.e. what features are meant here?

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[Mikhail Spivakov]

May I suggest that you give a good read to the R package vignette and try reproducing its results within R?

The relevant bit for this particular question is: http://regulatorygenomicsgroup.org/wp-content/uploads/Chicago_vignette.html#peak-enrichment-for-features

[Mikhail Spivakov]

These are chromatin features just for QC purposes. If you don’t have any for your cell type, just grab some datasets (ideally, both active and inactive features) for the same organism - it’ll help you a lot to check the quality of your data post-hoc.