Thank you very much, Rhead. We are re-running our pipeline and will let you know if we bump across any further issues around this.
cheers, Amit -----Original Message----- From: Brooke Rhead [mailto:[email protected]] Sent: Tuesday, May 03, 2011 6:40 PM To: Zarakhovich, Sophia Cc: Zhuang, Jun; [email protected]; Kulkarni, Amit (MPRI) Subject: Re: [Genome] (no subject) 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 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
