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
