optimizer FAQ

* Is it mandatory to run the optimizer module?

No. If the bkg_overlaps.gr file was not created by the optimizer module, GenomeRunner will calculate overlap statistics on the fly. However, this wil lengthen the run time, so be patient.

* Does the optimizer module process regulatory datasets filtered by score?

Yes. The optimizer module processes grsnp_db* folders with regulatory datasets filtered by score and creates the bkg_overlaps.gr files for each folder.

* I started the optimizer module but it takes too long. Can I terminate it without losing what has been pre-calculated?

Yes, you can safely terminate the process. The partially completed file bkg_overlaps.gr.tmp will be re-used and appended when the optimizer module is restarted.

* How the bkg_overlaps.gr file is structured?

It is a tab-separated text file containing the following information:

[Absolute path to the GF file]tab[Absolute path to the default background_one]:[bgs_obs]:[n_bgs],[Absolute path to the default background_two]:[bgs_obs]:[n_bgs] etc.,

where [n_bgs] is the total number of regions in the background file, and [bgs_obs] is the number of regions overlapping a genomic feature.