[Genome] briggsae annotation

[Ann Zweig]

Hello Toby,

	Right now there is no way to map the twinscan gene IDs to the CBG IDs 
for cb1.  Based on your inquiry, we have started a discussion with 
wormbase about solving this problem.  It looks like we will go with one 
of the following two solutions:

1. We may just lift the coordinates from the GFF file of the CBG genes 
(mapped to contigs) to the chrUn that we used for cb1 in our browser.

2. Or, we will wait for the C. briggsae gene set to be updated 
(scheduled for the next few months). There is currently a
gene prediction assessment going on for worms and there is an article 
about this on the WormBase wiki 
(http://www.wormbase.org/wiki/index.php/NGASP). The best method will be 
chosen for the basis for manual annotation at WUSTL.

	The wormbase help desk has asked me to let you know that you should 
contact them (help at wormbase.org) in the future if you would like 
information on the CBG change.

	Hope this is helpful to you.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



tw233 at bath.ac.uk wrote:
> Hey guys,
> 
> I've got a query I thought you might be able to help me out with:
> 
> I am trying to relate twinscan gene IDs as given by the UCSC browser 
> (eg cb25.fpc0003.0.26.a) to CBG IDs.
> but the UCSC IDs do not correspond in any obvious way to other gene 
> prediction IDs, including those for twinscan from other sources 
> (underlined below, taken from 
> ftp://ftp.wormbase.org/pub/wormbase/datasets/stein_2003/gene_prediction/cb.fa.gz)
> 
> 
>> CBG00175 CBP00013 (cb25.fpc0003.en7051a/cb25.fpc0003.tw120/cb25.fpc0003.fg93)
> 
> seeing that the twinscan track is the only one for Briggsae on the UCSC 
> browser there is no conversion file to relate the twinscan ID to other 
> formats.
> Any ideas how to solve this problem?
> 
> Thanks a lot
> 
> Toby
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