Hello Saatvik, The differences you are seeing are not caused by out date sequences, but appear to be differences between the blat CGI vs command line blat. It also might be due to the browser alignments being built with an older version of blat.
The code you are looking for is in: kent/src/hg/makeDb/genbank and it is documented here: kent/src/hg/makeDb/genbank/doc Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 12/08/10 10:56, Saatvik Agarwal wrote: > Hi UCSC, > > I've noticed that some of the UCSC refSeq mappings can be out of date since > the refGene track was made because the underlying RefSeq has changed. > Examples include NM_001002158 and NM_001002225 on danRer6. If I blat these > sequences to danRer6 now, I get slightly different coordinates. It seems > that when the Genbank/refseq update process is run, existing RefSeq mappings > are not checked or updated. While it would be nice to have that fixed, I > don't really mind it all that much and can live with that. > > However, for some research I was doing, I need to make an updated refGene > track from scratch and was wondering how UCSC did it. I did not find the > commands ennumerated in makeDb/doc and was wondering if they are made > available in the kent src somewhere. If you can tell me where they can be > found or send me a shell script, I'd really appreciate it. > > Thanks, > Saatvik > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
