Re: [Gmod-ajax] Loading GFF trouble

[Colin D. <col...@ho...>]

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_COLDidn'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 3S.aur_COL       BOWTIE  .       2474533 2474567 1       +       .       ID=5_BWCOjxwXsN1/1
S.aur_COL       BOWTIE  .       1980530 1980564 3       +       .       ID=7_NZCOjxwXsN1/1S.aur_COL       BOWTIE  .       2115669 2115703 3       +       .       ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       2232159 2232193 3       +       .       ID=7_NZCOjxwXsN1/1S.aur_COL       BOWTIE  .       530658  530692  3       -       .       ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       574288  574322  3       -       .       ID=7_NZCOjxwXsN1/1S.aur_COL       BOWTIE  .       579500  579534  3       -       .       ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       2721172 2721206 1       +       .       ID=3_2VCOjxwXsN1/1S.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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