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Published 20 hours ago • verified publisher icon Arkadiy-Garber

geneSummary file

Open JBuongio opened this issue 2 years ago • 3 comments

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

JBuongio avatar Jun 30 '22 15:06 JBuongio

Hi Joy,

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

Thanks, Arkadiy

Arkadiy-Garber avatar Jun 30 '22 20:06 Arkadiy-Garber

Hi Arkadiy,

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

Best, Joy

JBuongio avatar Jul 01 '22 01:07 JBuongio

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

MightyMaus avatar Jul 04 '22 09:07 MightyMaus