gmod-ajax

[Gmod-ajax] how I set multiple reference sequences

[du z. <adu...@gm...>]

Hi, here is my question. As mentioned in the tutorial use the command "$
bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa" to set
reference sequences.
My problem is that presuming that I have three fasta files representing
three chromosomes, and how I set these reference sequences (using
bin/prepare-refseqs.pl ?) ?
And what else config files should I prepared for these three refseq?
Thank you~

-- 
杜舟 (name in Chinese)
Zhou Du (name in English)
PhD candidate in Bioinformatics
College of Biological Sciences
China Agricultural University
Beijing, China
Lab phone: +86-(010)-62731214

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

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

On 08/06/2009 07:55 PM, du zhou wrote:
> My problem is that presuming that I have three fasta files
> representing three chromosomes, and how I set these reference
> sequences (using bin/prepare-refseqs.pl ?) ?

Hello,

You can just run bin/prepare-refseqs.pl three times, once for each fasta
file. I added some code to handle this case better in mid-June; if your
JBrowse is older than that, then pull the current version.

Please let us know if it works for you; if it doesn't then there may be
a bug.

Mitch

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

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

On 08/07/2009 02:14 AM, du zhou wrote:
> Thank you for reply.
> Yes, it works. One more question is that can I set the refseq without
> fasta files of DNA sequences? In other word, can I use the GFF file
> only as refseq?
> I tried ”bin/prepare-refseqs.pl --gff
> docs/tutorial/data_files/volvox.gff3“, but it gave out "found no ref
> seqs at bin/prepare-refseqs.pl line 199.", and same happened when I
> tried "bin/prepare-refseqs.pl --gff
> docs/tutorial/data_files/volvox.gff3 --noseq"
> Thank you~

If you have a GFF file with sequence-region directives in it, you can
use that file with
bin/prepare-refseqs.pl --gff <file> --refs <comma-separated list of ref
seq names>

See the "Other Syntax" section of
http://www.sequenceontology.org/gff3.shtml
for details about sequence-region.

I'll document that better, and maybe add an example file to make it
easier to demonstrate how to use it. You're right that the example GFF
file that we currently have doesn't work for that use.

I added that functionality originally because I wanted it for testing,
but I'm interested in real use cases. Is there no sequence for your
organism? Or are your users just not interested in the sequence? What
data are you starting from, and what format is it in?

Regards,
Mitch

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