Hello Liz, There are two differences between the human (hg18) refGene.txt file and the rat (rn4) refGene.txt file. The first difference is that the tables are in slightly different formats. The human refGene table contains extra information that we use here to indicate codon frames when items are displayed in the "RefSeq Genes" track. The rat table does not have this extra information. You can see the differences in the table formats by going to the track controls page for that track and clicking "view table schema", or by clicking the links below:
http://genome.ucsc.edu/cgi-bin/hgTables?db=hg18&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_doSchema=describe+table+schema http://genome.ucsc.edu/cgi-bin/hgTables?db=rn4&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_doSchema=describe+table+schema The other difference between the human and rat refGene tables is that they were created using slightly different parameters for alignment to the reference genomes. The parameters used for rat were slightly looser, and allowed for more alignments to be kept than for human. The parameters for all of the different assemblies are chosen to get the best results in light of the quality of the reference genome. -- Brooke Rhead UCSC Genome Bioinformatics Group On 06/04/09 06:53, Worthey, Elizabeth A. wrote: > Hi. I'm having problems using the Rat refGene.txt file in a sequenc > eassembly 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
