Hello Giulio, What is likely happening is that you're asking for so much data at one time that the servers time out. The way around this problem is to run your queries in smaller chunks, such as doing each chromosome separately.
>From what you are describing it looks like you might try the following method >to get the data you are looking for: Go to the Table Browser, "Tables" on the blue bar on the top of the main page. Leave the default settings but change group to "Variation and Repeats", track to "SNP Arrays" and table to "snpArrayIllumina1M". Change the position to just one chromosome, or to a subregion you are interested in. for "output format" choose "selected fields from primary and related tables", then click "get output". On the next page, under Linked Tables click the box next to "hg18.snp129" and click "Allow Selection from Checked Tables". Now you are able to select which columns from hg18.snp129 that you would like to retrieve alongside your Illumina array data. When you've selected the fields you want from both tables, click "get output". This should get you the data you're looking for. You might also have a look at the Galaxy website to do joins and intersections for you: http://main.g2.bx.psu.edu/ I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- "Giulio Genovese" <[email protected]> wrote: > I am trying to download a list of SNPs from the > hg18.snpArrayIllumina1M > database integrated with fields from the hg18.snp129 database but the > > website seems to repeatedly fail at delivering the table. > > Without integrating the two databases everything works fine. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
