Hi Mircea

I think you have to careful about how you are selecting. If you select the
first CDS in the sequence and then use 'Select'->'Same key' and then use the
Auto Create Gene Names option the numbering will be from left to right. Then
you do the same for 'gene' (using the same start and increment values as
before) and for the RNAs. The numbering then should be consistent.

Regards
Tim

On 18/02/2014 17:41, "Podar, Mircea" <pod...@ornl.gov> wrote:

> Hello,
> 
> I am having difficulties filling in fields for a microbial genome. I have a
> Genbank format file that already has genes called etc. I wanted to do a
> renumbering of the genes and CDSs and RNAs so I deleted the original
> "locus_tag" from the file. Then I applied Automatically Create Gene Names
> and used "locus_tag" as a target. All good. But I also need the same locus
> tag to go on the CDS/RNAs as well. If I have selected all genes and then
> apply the select "features matching qualifier" the selection shifts ao all
> CDS and RNA genes. Perfect. Now if I want to do again the  Automatically
> Create Gene Names to apply a locus_tag on these it does it but the ordering
> is all messed up (i.e. I get locus tag 1 for the CDS and locus tag 2 for the
> gene of that CDS and vice-versa, makes no sense and doesn't seem to be
> linked with the strand orientation). How can that be fixed? Unfortunately a
> very simple feature, to copy the locus tag from gene to CDS seems to be
> missing, or at least I havent figured out how to do it for all genes at
> once.
> 
> Unfortunately the locus tag is needed on both gene and CDS in order to
> import the file into Sequin for GenBank submission. Its much harder to
> submit a genome nowadays than to actually sequence it...
> 
> 
> Thanks!
> 
> 
> 
> Mircea
> 
> 
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