Hi again Sophia, There indeed *was* a problem that I had not been aware of with the old files. The problem has been corrected, and new files (dated today) are available now on http://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/ .
Sorry for the inconvenience, and please let us know if you have any further questions by emailing [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 05/03/11 15:00, Brooke Rhead wrote: > Hi Sophia, > > These tables (along with many others generated from GenBank data) are > updated on our website nightly. The tables are copied to our downloads > server (http://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/) once a > week, on Sunday. > > So, if you look at the Rat mRNAs track in the Genome Browser, or view > the tables with the Table Browser, you will see both the all_mrna and > the mrnaOrientInfo tables from 2011-05-02. However, the tables you are > using are not necessarily out of sync, as mrnaOrientInfo contains > information for both mRNAs and RefSeq Genes, so it's possible for > mrnaOrientInfo to be newer than all_mrna. > > I was not able to see your list of comparisons of start coordinates, as > our mailing list software strips attachments, but if you would like to > send a small example of something that looks incorrect, we could look > into it further. > > Regarding your second question, yes: 'Canis familiaris' has been > replaced by 'Canis lupus familiaris' in the tables from GenBank. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > On 05/02/11 06:48, Zarakhovich, Sophia wrote: >> Hello! >> >> I have a question about April 18th release of mrnaOrientInfo.txt and >> all_mrna.txt files in the Rat assembly. It seems that while >> mrnaOrientInfo.txt has been updated on April 18, the all_mrna.txt file >> has remained the same since April 11th update and some of the genomic >> coordinates do not match. I was wondering, would it be possible to >> update all_mrna.txt to match the new mrnaOrientInfo.txt file? Thank >> you. As a reference, I included a list of comparisons of start >> coordinates for the two files (field 17 in the all_mrna.txt file and >> field 3 in mrnaOrientInfo.txt file). >> >> Also, is there a reason 'Canis familiaris' is absent from organism.txt >> file in the Dog assembly? Has it been replaced by a different >> nomenclature? >> >> Best regards, >> >> Sophia Zarakhovich >> >> <<start_coord_comparison>> >> Notice: This e-mail message, together with any attachments, contains >> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, >> New Jersey, USA 08889), and/or its affiliates Direct contact information >> for affiliates is available at >> http://www.merck.com/contact/contacts.html) that may be confidential, >> proprietary copyrighted and/or legally privileged. It is intended solely >> for the use of the individual or entity named on this message. If you are >> not the intended recipient, and have received this message in error, >> please notify us immediately by reply e-mail and then delete it from >> your system. >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
