Hi Laura, It looks like the Table Browser is timing out on this large query. There are a couple of ways you could work around this:
You could try limiting the output by pasting a list of the RefSeq identifiers that you are interested in. When I followed the instructions in the link you sent but pasted in a single identifier, I was able to get results. Another way to get the information you want would be to download the two tables you are working with from our downloads server: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ (this page takes a while to load) Specifically, you would need: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gbStatus.txt.gz Then you could join the two tables yourself. If you don't have a good way to accomplish a join of the tables, you could use Galaxy: https://main.g2.bx.psu.edu/. You would need to first fetch each of the tables separately using the "UCSC Main table browser" link (under "Get Data"), and then join them on the refGene.name/gbStatus.acc fields using the "Join two Datasets" link (under "Join, Subtract and Group"). If you have any questions about using Galaxy, please contact their helpdesk at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 6/1/12 1:53 PM, Laura Smith wrote: > Hello Steve, > > Thank you very much for your reply. Based on your suggestion, I decided to download the newest REFSEQ and ENSEMBLE transcripts from UCSC Browser with all of the gbstatus subfields. > > I have tried to download these files with the gbstatus fields, > however I keep getting error from UCSC genome browser website. I am following the directions listed here: > > https://lists.soe.ucsc.edu/pipermail/genome/2011-September/027099.html > > > > Is there something I am doing wrong perhaps? Please see the attached 2 files for the screenshots of the error messages from UCSC browser. > > > If not, since I am not able to download these files, would it be possible for you to please send me or provide me a link to the latest Refseq and Ensemble transcripts please with all of the gbstatus subfields? > or if you could please let me know how I can download them with the gbstatus fields, I would very much appreciate it. > Thank you, > Laura > > > > > ________________________________ > From: Steve Heitner<[email protected]> > To: 'Laura Smith'<[email protected]>; [email protected] > Sent: Wednesday, May 30, 2012 10:47 AM > Subject: RE: [Genome] Downloading old refseq and ensemble transcripts with > the "version numbers" in the accession IDs. > > Hello, Laura. > > As you mentioned, the refGene table does not actually list the Genbank > version number. The hg19.gbStatus.version field does list the version > number, but the problem is that this is the current version number and not > necessarily the version that was current as of June 23, 2011. There is also > a field called hg19.gbStatus.modDate that lists the last modified date, but > there are two problems with this. First, our modDate does not necessarily > coincide precisely with the official Genbank version date (e.g., our modDate > for NM_021219.2 is March 21, 2012 while Genbank lists it as April 21, 2012). > Also, if the particular transcript you are looking at is a version 3 (e.g., > NR_001458.3), the gbStatus table does not keep a history of previous > versions and modDates, so there is no way to know whether it was NR_001458.1 > or NR_001458.2 on June 23, 2011. > > We do not keep histories of the refGene table, so there is no June 23, 2011 > version of refGene that we can direct you to. There is no easy way to get a > snapshot of the data as it existed on June 23, 2011. It is possible to look > directly at Genbank to find the dates corresponding with the various > transcript versions (e.g., http://www.ncbi.nlm.nih.gov/nuccore/NM_021219.1 > shows that NM_021219.1 was released on April 24, 2002 and > http://www.ncbi.nlm.nih.gov/nuccore/NM_021219.2 shows that NM_021219.2 was > released on April 21, 2012), but if you have a large number of IDs, this > would be very tedious without some kind of custom script. > > Please contact us again at [email protected] if you have any further > questions. > > --- > Steve Heitner > UCSC Genome Bioinformatics Group > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Laura Smith > Sent: Tuesday, May 29, 2012 1:56 PM > To: [email protected] > Subject: [Genome] Downloading old refseq and ensemble transcripts with the > "version numbers" in the accession IDs. > > Hello, > > I have been using the refseq transcripts and ensemble transcripts downloaded > from UCSC genome browser table on June 23 2011. The transcript IDs in these > datasets that were downloaded from UCSC do not have the version numbers > (such as NM_134564.2) where ".2" is the version number after the period. > > However, recently, it turns out that I need to have the version numbers of > each transcript. So, I tried to look for them and download them using the > info provided here, however there is no way for me to choose the refseq > transcripts for the date June 23 2011: > > https://lists.soe.ucsc.edu/pipermail/genome/2011-September/027099.html > > > Would it be possible for you to please send me the refseq and ensemble > transcripts for June 23 2011 from your archives please which includes the > version numbers for each transcript in them? > > > Or if there is a way that I could access this data myself, if you could > please let me know I would very much appreciate it. > > > Thank you, > Laura > _______________________________________________ > 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
