Hello Jelti - The cds information can be found in the table "cds". To get there from the track's primary table, use the Table browser to navigate:
primary table: dm3.all_mrna link path: dm3.all_mrna.qName -> dm3.gbCdnaInfo.acc dm3.gbCdnaInfo.cds -> dm3.cds.id cds defined here: dm3.cds.name Please note that this information comes from the Genbank report and may not be available for all mRna sequence (in particular, for other species). This also means that the coordinates are 1-based fully-closed, not 0-based half-open(data parsed into the normal UCSC coordinate system are 0-based half-open). If you need help about this, please ask. Example output using the Table browser dm3, track=D. melanogaster mRNAs, table=all_mrna, region=chr2L:826001-851000 , output "selected field from primary and related tables". The fields I picked are noted in the output. #dm3.all_mrna.qName dm3.gbCdnaInfo.id dm3.gbCdnaInfo.cds dm3.cds.id dm3.cds.name U57816 477804 81074 81074 1184..2416 AY119614 449899 70763 70763 732..2378 FJ636318 2571133 296841 296841 17..1663 FJ631433 2566248 295951 295951 17..>1660 BT072822 2376782 6713 6713 <1..1033 AF097364 420464 59138 59138 959..2551 AY119526 449811 70695 70695 99..1442 FJ635889 2570704 73432 73432 17..1360 FJ631010 2565825 295972 295972 17..>1357 BT099783 2624400 113374 113374 <1..1879 BT099777 2624394 29574 29574 <1..1036 Note that for some larger genomes or for xenoMrna tracks, the query may be too large for the Table browser. For those cases, download the text files from the Downloads server and use your own tools to perform the joins. Follow-up questions are welcomed, Jen ps. We are aware of the access problems to the archives. This appears to be browser dependent. We are recommending IE or Safari right now until the problem is resolved. Very sorry for the inconvenience. --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/17/10 1:06 PM, Jeltje van Baren wrote: > Hello browser people > > First off, I've tried searching for this in the genome mailinglist archives. > I did get a list of links, but none of them worked, they all result in > Secure Connection Failed > Peer's Certificate has been revoked. > (eg https://lists.soe.ucsc.edu/pipermail/genome/2004-July/005062.html) > > So I know this has been asked before, but I couldn't find an answer in the > cached results that I could access. > > I want to download the mRNA track from dm3 with the thickStart and thickEnd > preserved. Right now, the fields are set to chromStart and chromEnd, but I > want to know the ORF that can be seen on the Browser. > How do I do that? > > Best, > > -Jeltje > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
