Hi Pauline, This has been extremely helpful, I do have a couple of question thou.
When exporting the affyU133Plus2 data to BED I realized the info for chromStarts is not exactly the same as qStarts, I wrongly assumed it was the same, that's why taking it directly from mysql didn't produce the same output, out of curiosity and for future reference could you tell me why this difference? I have never used Galaxy, I'll try to use it for this now, but it seems bedMergeExpData would fit better for my need, as I would like to have the option os running my data through a script pipeline, I compiled the utility and I get this from the help: $ bedMergeExpData bedMergeExpData - Merge probe position information (bed table) with an expData table and make a new bed file from that. usage: bedMergeExpData database.expDataTable database.bedTable merged.bed As the developer point me, I need to get the BED data I got from the table browser into a mysql table, that's fine with me, but what about the format for expDataTable?, could you point me to any documentation with a description? Thanks, -- Carlos Borroto Baltimore, MD On Fri, Apr 29, 2011 at 2:54 AM, Pauline Fujita <[email protected]> wrote: > Hello Carlos, > > One of our developers had this to say about your question: > > The coordinates you are using from the annotation are indeed not at the > precision you want. They're essentially the region of the gene, introns > included. You will want to download a BED12 of Affy data and append your > data in columns 13-15. The U133+2.0 seems to be based on multiple gene sets: > refseq and ensembl, so it's just a matter of making a bed12 for each probe. > > To do so, go to the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) > and select: > > clade = Mammal > genome = Human > assembly = Feb 2009 (hg19), or hg18 if desired > group = Expression > track = Affy U133Plus2 > table = affyU133Plus2 > region = genome > identifiers, filter, intersection, correlation = <don't change> > output format = BED - browser extensible data > output file = something.bed.gz > file type returned = gzip compressed > ... then click "get output" > > To append your data to the BED12 you have obtained you can try using the > kent source utility bedMergeExpData but be advised that this is designed for > working on tables rather than files. Alternatively you might try joining the > data using the utilities at Galaxy (http://galaxy.psu.edu/). If you decide > to use Galaxy you can take advantage of the "Send output to Galaxy" function > in the table browser. > > Hopefully this information was helpful and answers your question. If you > have further questions or require clarification feel free to contact the > mailing list at [email protected]. > > Best regards, > > Pauline Fujita > > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > > On 4/20/11 7:46 AM, Carlos Javier Borroto wrote: >> >> Hi, >> >> I'm working on getting a microarray track into our local mirror, >> following directions from the wiki page I was able to do so. >> >> The coordinates I was using initially were from this file: >> >> http://www.affymetrix.com/analysis/downloads/na31/ivt/HG-U133_Plus_2.na31.annot.csv.zip >> >> But this coordinates expand very large areas, I would like to only >> display data for the exon areas like in "GNF Atlas 2" track, I found I >> could add "expDrawExons on" to activate this option, but after >> selecting it I still don't get the same results, so I focus my >> attention into getting blockCounts, blockSizes and chromStarts right, >> I tried to take the coordinates for the probes from affyU133Plus2 >> track, that didn't do the trick either ask I could see the coordinates >> in affyU133Plus2 and gnfAtlas2 aren't exactly the same, my last >> resource was to use the coordinates directly from gnfAtlas2, but that >> doesn't cover all of the probes we have. Is there a better way to get >> this right? >> >> Thanks for your help, >> -- >> Carlos Borroto >> Baltimore, MD >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
