geneSummary file

[JBuongio]

Hi Arkadiy,

Just a quick question -- are the outputs in the geneSummary files showing all encoded HMM hits and their ORFs or are these hits that are both encoded and have coverage in the supplied BAMs? Thanks!!

Best,
Joy

[Arkadiy-Garber]

Hi Joy,

Good question! Those files should contain all the hits, regardless of the coverage.

Thanks,
Arkadiy

[JBuongio]

Hi Arkadiy,

Great, thanks! Any suggestions on how to cross-check the coverage of ORFs? If not, no worries!!

Best,
Joy

[MightyMaus]

Hi Arkadiy

We compiled FeGenie last week and are now running our databases through it to find iron related genes. We see duplicate results for each contig screened, from two slightly different processes that yield the same result. In other words, we get a repeated hit for a specific gene on a contig - the hits are identical but reported twice. Did we compile incorrectly or is this on purpose - if so, why?

Thanks
Michelle