Hi, I'm trying to retrieve regions that are aligned to oRegAnno annotations in several species. Initially I've started with mouse. I can use the UCSC DAS capability to retrieve the oRegAnno features and retrieve the DNA sequences for them. I can't work out how to get to bases in other species using DAS or any other method that I can script.
I found this advice from Jennifer Jackson in an old post on this newsgroup: > Using the tools at UCSC, the Table Browser will return blocks of Conservation > MAF results, but not specific bases. However, by sending the data over to > Galaxy, "slices" of the Conservation track's MAF alignment can be retrieved > in batch using a custom track of intervals (down to a single base). > > To do this: > > 1) Create and load a custom track in BED format of the genome positions of > interest > 2) Send the custom track to Galaxy by extracting it from the Table browser > and checking Galaxy as the output choice > 3) Send of the Conservation track's MAF alignment data to Galaxy using same > method (you may need to subset this by chromosome to improve > speed/performance) > 3) Use the Galaxy tools: Fetch Alignments -> Extract MAF blocks given a set > of genomic intervals > > UCSC help is as follows: > > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser > http://genome.ucsc.edu/FAQ/FAQformat#format1 > http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms > > Galaxy help is available at their web site if you have questions about the > tools. > I tried this but it took hours just to load the conservation track for mouse chromosome 10 into galaxy. I have several organisms, each with many chromosomes. Is there a better way to do it? It's frustrating because with a few clicks on the Genome Browser web interface I can retrieve the information I need for one particular region but I can't work out how to write a script to retrieve it. Thanks in advance, John. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
