Renamed contigs?

[JBuongio]

Hi Arkadiy,
Thank you for all that you do! I am noticing that FeGenie renumbers/names contigs within individual MAGs' depth files. For those of us who cross-reference output from different tools, like anvi'o, would it be possible to retain the original contig names? For example, if I'm looking at output about c_000000001 from anvi'o and I use the same input fastas for FeGenie analysis, it would be really great to have that same c_000000001 contig be tied to the same MAG that anvi'o analyzed. Does this make sense? I double-checked that the input MAGs fastas for FeGenie were those made by the SUMMARIZE program within anvi'o.
Thank you!!
Best,
Joy

[JBuongio]

I should say also, the contig names in the geneSummary-clusters.csv file and the depth files don't match each other, making it a little hard to check if a contig that has been identified to contain a gene cluster is covered in the metagenome/transcriptome (although the .csv does tell you which MAG it came from). Thanks! =)

[Arkadiy-Garber]

Hey Joy,

Thanks for the note - hope you are well! :)

I was not aware that FeGenie renames contigs. As far as I remember that is not the intended function. Could you please attach or send me an example of a .depth file where the contig names are changes, perhaps with the geneSummary.csv file for reference.

Thanks!
Arkadiy

[JBuongio]

Thank you! I've placed in the FeGenie_troubleshooting Google Drive folder that we have used before files that should help: geneSummary.csv, geneSummary-clusters.csv, the bin fastas, and the depth files for each bin.
You'll notice that while the geneSummary files have the contig names that correlate to the original bin fasta contig names, the contig names in the depth files all restart at c_000000000001. When I grep this contig name in the bin_dir, it should only appear in MAG-19: `(fegenie) $ grep "c_000000000001" *fa

Lentisphaerae_bacterium_MAG-19-contigs.fa:>c_000000000001`

Thank you so much for your time.

[Arkadiy-Garber]

Hey Joy! So sorry for the delay in getting to this - been a busy month for me, but I'll have some time coming up to get to this issue.

Thanks for your patience!
Arkadiy