Hello Liz, We have currently have no plans to add this information for assemblies other than mouse and human. Are the codon frames actually needed by the Roche 454 assembly software, or is it just expecting the input data to be formatted in a certain way? I'm thinking that if the information in the "exonFrames" field is not being used, perhaps dummy columns could be added to the rat refGene.txt file so that it will be accepted by the software.
-- Brooke Rhead UCSC Genome Bioinformatics Group On 06/10/09 20:16, Worthey, Elizabeth A. wrote: > Hi. Sorry it looks like the answer passed through my inbox without me > seeing it: > https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019171.html . It > is undoubtedly the change in format for codon frames that renders the > file unusable with the Roche 454 assembly software. Is there any way > that this information could be incorporated into the rat file? Thanks > again, > > > > Liz Worthey > > Senior Research Scientist > > Human and Molecular Genetics Center > > Bioinformatics Program > > Medical College of Wisconsin > > [email protected] > > Tel: 414-456-7426 > > Fax:414-456-6595 > > M4677 > > http://rgd.mcw.edu <http://rgd.mcw.edu/> > > > > From: Worthey, Elizabeth A. > Sent: Wednesday, June 10, 2009 4:47 PM > To: '[email protected]' > Cc: 'Brennan Decker'; 'Barthalomew Sillah' > Subject: RE: Rat refGene.txt file > > > > Hi. Thanks again for providing such a great resource - I was curious if > there had been any progress with the question below. Also since I will > be out of the office starting tomorrow I am cc'ing two colleagues who > will be working on this project. If a response could be sent to all thee > e-mail addresses that would be great. After looking at the format of the > human and rat refgene.txt files I do see a number of differences which > I'm assuming are causing the error I get in my third party software; > could you confirm that the files are different in format and, if that is > the case, let me know if (and when) there are plans to provide a rat > file of the same format as the human file. Thanks in advance, > > > > Liz Worthey > > Senior Research Scientist > > Human and Molecular Genetics Center > > Bioinformatics Program > > Medical College of Wisconsin > > [email protected] > > Tel: 414-456-7426 > > Fax:414-456-6595 > > M4677 > > http://rgd.mcw.edu <http://rgd.mcw.edu/> > > > > From: Worthey, Elizabeth A. > Sent: Thursday, June 04, 2009 8:53 AM > To: '[email protected]' > Subject: Rat refGene.txt file > > > > Hi. I'm having problems using the Rat refGene.txt file in a sequence > assembly using the Roche gsMapper application. I have no problems using > the same file created for H. sapiens, and download these files for > different organisms through the same process. Could you let me know > whether there are differences between the files (the creation method, > underlying tables etc.) for the rat and other organisms? Thanks in > advance, > > > > Liz Worthey > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
