Re: [Gmod-ajax] how I set multiple reference sequences

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

On 08/08/2009 11:06 PM, du zhou wrote:
> In the tutorial, I know that I can set additional tracts by using 
> "biodb-to-json.pl" multiple times. Nevertheless, I have another 
> question that is it possible to delete tracks after config if I don't 
> like them in the future? Or I should rebuild a new Jbrowse html directory?
>

There's no program written to do it, but you can do it by hand.  You 
have to edit data/trackInfo.js to remove the relevant entry, and 
(optionally) delete all the directories:

data/tracks/*/<trackname>

Also,

On 08/07/2009 04:34 AM, du zhou wrote:
> I tried this "bin/prepare-refseqs.pl --gff 
> docs/tutorial/data_files/volvox.gff3 --refs gfftest", but it still 
> warned "found no ref seqs at bin/prepare-refseqs.pl line 199.".

Right, that won't work.  We don't currently have an example in the 
source tree that can be used to demonstrate that functionality.  I've 
attached a gff file that I've used to do this for fly.  I used it like this:

bin/prepare-refseqs.pl --gff ~/data/chroms.gff

> What are "ref seq names"? What are they use for? I am a bit confusing.

Chromosome names, usually, or contig names.  prepare-refseqs.pl uses the 
names to look up the reference sequence in the data source.

Hope that helps,
Mitch