Re: [Gmod-ajax] Loading GFF trouble

[Martin A. H. <ma...@ma...>]

Right, that did the trick.

But clicking on a feature shows ID undefined? and strand is shown as either
1 or -1.

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




Martin

On Mon, Oct 19, 2009 at 1:27 PM, Colin Davenport <col...@ho...>wrote:

>  Hi Martin,
>
> I had a similar problem.
>
> I think this should help : you need to modify the GFF header
> and add a line
>
> ##sequence-region scf1117875581239 1 719819
>
> Source was this tutorial
>
> http://gmod.org/wiki/JBrowse_Tutorial#Moving_work_to_the_client
>
> Hope that helps
>
> Colin
>
>
>
>
>
> ------------------------------
> Date: Mon, 19 Oct 2009 12:33:24 +0200
> From: ma...@ma...
> To: gmo...@li...
> Subject: [Gmod-ajax] Loading GFF trouble
>
>
> Hello,
>
>
> I am trying to visualize some Bowtie hits of small sequences mapped to a
> bacterial genome.
>
> I have Apache and Jbrowse up and running.
>
> I have loaded the genome sequence using prepare-refseqs.pl from the www
> root - and it is visible in Jbrowse.
>
> Now, loading some GFF3 data gives trouble:
>
> bin/flatfile-to-json.pl -gff /Users/maasha/DATA/Assembly/foo.gff
> --tracklabel test1 --key 'human readable test'
>
> working on seq S.aur_COL
> Didn't find a segment with name S.aur_COL
> Use of uninitialized value in string eq at bin/flatfile-to-json.pl line
> 178, <GEN2> line 24.
>
>
> The GFF data looks like this (may be malformatted?):
>
> ##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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