Re: [Gmod-ajax] Loading GFF trouble

[Mitch S. <mit...@be...>]

Martin A. Hansen wrote:
> But clicking on a feature shows ID undefined? and strand is shown as 
> either 1 or -1.

The ID thing was kind of a mis-labeling; JBrowse can optionally keep 
track of a separate "name" and "ID", but sometimes identifiers become 
names and vice versa.  I clarified the click-popup to show name and ID 
separately, and modified flatfile-to-json.pl to include the ID from the 
GFF as the ID in JBrowse, rather than the autogenerated one that 
Bio::DB::SeqFeature::Store creates.

> Also, I have a feature that is full chromosome length (2.8M) and 7 
> that are 0.5M. Strange?

The full length feature is from the sequence-region header; now that you 
don't need that anymore, you can leave it out.  Alternatively, you can 
use the --type command line option to filter out the full length feature.

The long features are probably due to the fact that you have several 
features with the same ID.  I believe the bioperl code is merging them 
together.

Mitch

>
>
>
>     ##gff-version 3
>     S.aur_COL       BOWTIE  .       2474533 2474567 1       +      
>     .       ID=5_BWCOjxwXsN1/1
>     S.aur_COL       BOWTIE  .       1980530 1980564 3       +      
>     .       ID=7_NZCOjxwXsN1/1
>     S.aur_COL       BOWTIE  .       2115669 2115703 3       +      
>     .       ID=7_NZCOjxwXsN1/1
>     S.aur_COL       BOWTIE  .       2232159 2232193 3       +      
>     .       ID=7_NZCOjxwXsN1/1
>     S.aur_COL       BOWTIE  .       530658  530692  3       -      
>     .       ID=7_NZCOjxwXsN1/1
>     S.aur_COL       BOWTIE  .       574288  574322  3       -      
>     .       ID=7_NZCOjxwXsN1/1
>     S.aur_COL       BOWTIE  .       579500  579534  3       -      
>     .       ID=7_NZCOjxwXsN1/1
>     S.aur_COL       BOWTIE  .       2721172 2721206 1       +      
>     .       ID=3_2VCOjxwXsN1/1
>     S.aur_COL       BOWTIE  .       575753  575787  3       +      
>     .       ID=1_GbCOjxwXsN1/1
>
>
>     refseq.js looks like this:
>
>
>     refSeqs =
>     [
>        {
>           "length" : 2809422,
>           "name" : "S.aur_COL",
>           "seqDir" : "data/seq/S.aur_COL",
>           "start" : 0,
>           "end" : 2809422,
>           "seqChunkSize" : 20000
>        }
>     ]
>
>     I cannot tell what version or revision my Jbrowse installation is
>     (how do I find out?).
>
>     So what is this segment error? And how do I resolve it?
>
>
>
>     Cheers,
>
>
>
>     Martin
>
>
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