Hello Maxim, You are right, the MAF data can be restricted by organism using the Table browser only under special conditions and the output is just fasta sequence (not MAF stacked alignments, genePred format is required). The download data will be necessary for custom data that does not meet these conditions. Filter it and upload back into the UCSC Browser and/or Galaxy.
Some additional information: For hg18/hg19, general table help: 1) table browser, set clade, genome, assembly, group = Comparative genomics, track = Conservation - hg18 will have a 44-way, hg19 will have a 46-way 2) all tables (subtracks, etc.) will be in the "tables" pull down menu. leave default for now. 3) click on "view table schema" to link into the page with the main table defined and the linked tables listed. You can click on any of these tables to view their schema. The common keys are noted. Just so that you know (even though I do not think this is the correct method for your particular data, as it is non-coding), to subset a MAF alignment by genome(s) in the Table browser, start with a track containing your data in genePred format (UCSC Genes or other), then select as output "CDS Fasta ......". Then submit. Here the output can be filtered by species, the same as in the Conservation track's control page. Again, note this is fasta sequence - not MAF alignments. For most cases, sending the MAF data from the Table browser to Galaxy for more processing or by using the download data and your own tools (or utilities from the kent source tree) rea the best solutions for very detailed queries. http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities (brief use summary per utility) http://genome.ucsc.edu/FAQ/FAQdownloads#download27 (readme files in download explain how to install/use) Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Maxim" <[email protected]> wrote: > From: "Maxim" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Tuesday, December 15, 2009 3:34:22 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] extraction of conservation scores for specific genomes > > Hi, > > sorry, but it appears I cannot find the part in the table browser > where to > filter tables, under > > group: comparative genomics > track: eg 28-Way Cons > tables: phastCons28way and others > > When I try to use the filter I do not find any setting that allows > specification of any tables but rather settings on positional/score > information. > > Under output format I have selected MAF. > > I can create an intersection with my custom bed tracks and get > conservation > scores for those intervals. > > But I do not find where to subset specific tables. I can do this > within the > real browser and get a nice display of conservation score for the > chosen > genomes. > > Could you please point me at the correct place to go! > > Kind regards > > Maxim > > > > > 2009/12/14 Jennifer Jackson <[email protected]> > > > Hello, > > > > The Conservation track MAF alignment can be limited by species by > using the > > filter function and adding in the desired assembly name (one) to > create a > > pairwise alignment. This result can be exported to Galaxy and > intersected > > with your regions (the Table browser cannot retrieve portions of > alignment > > block - all or none is the result if an overlap or region query is > made). > > > > The chain or net track can be used, but used alone, they do not > represent > > the same type of data result. For a chain or net track, the > comparison is > > from species A->B ordered alignments. In the conservation track, the > data is > > filtered for A<->B synteny. If you use just chains or nets, you will > likely > > need to use the data as an input to your own processing, not as a > final > > result. > > > > See the phyloP subtrack information concerning scores generated by > PHAST. > > You should be able to create scores for any subset of the data that > is > > already aligned. Be sure to note that the new 46-way is available in > the > > updated Human GRCh37 (hg19) assembly. > > > > The Conservation MAF or PhyloP data can also just be downloaded: > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/ > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/ > > > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP46way/ > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/ > > > > Some prior mailing list questions that provide related information: > > https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019178.html > > https://lists.soe.ucsc.edu/pipermail/genome/2009-July/019526.html > > https://lists.soe.ucsc.edu/pipermail/genome/2009-July/019616.html > > > > We hope this helps, > > Jennifer > > > > > > ------------------------------------------------ > > Jennifer Jackson > > UCSC Genome Bioinformatics Group > > > > ----- "Maxim" <[email protected]> wrote: > > > > > From: "Maxim" <[email protected]> > > > To: [email protected] > > > Sent: Sunday, December 13, 2009 3:22:47 AM GMT -08:00 US/Canada > Pacific > > > Subject: [Genome] extraction of conservation scores for specific > genomes > > > > > > Hi, > > > > > > I wonder whether there is a chance to extract conservation scores > via > > > UCSC, > > > especially conservation between distinct genomes. In my case I > have a > > > lot of > > > transcription factor binding sites (in GALAXY and as custom tracks > in > > > UCSC > > > browser). I know how to use the table browser to extract for > example > > > PhastCons scores. But this seems to be limited to 7 or 8 tables > > > encompassing > > > 12-44 different genomes. Does this mean I have to produce my own > > > conservation scores in case I'm just interested into the 3 genomes > of > > > human, > > > rat and mouse? > > > > > > The other option would be to extract pairwise sequence alignments. > Is > > > this > > > possible with UCSC, let's say starting with .bed files with 5000 > 20bp > > > intervals, to extract the pairwise alignments of those human > regions > > > with > > > mouse and/or rat genomes? > > > > > > I'd be glad in case someone could point me at the right > direction. > > > > > > Maxim > > > _______________________________________________ > > > Genome maillist - [email protected] > > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
