Daniel, I'm not sure I'm following the steps entirely. It looks like here you are trying to send the entirety of the 28-way alignments from the genome browser to Galaxy. This would require moving more than 30 gigs of data from the table browser to Galaxy, that would take a very long time. Try the following steps instead: 1) Upload your intervals using Get Data -> Upload File. Ensure the file format of the new dataset is "bed" or "interval". 2) Go to Fetch Sequences and Alignments -> Extract MAF Blocks (*not* Extract User MAF Blocks). On the first page, select your dataset and click "Next Step". On the second page, choose "28-way multiz" and click Execute. For 1500 intervals this shouldn't take more than a minute or so. Let me know how it goes. Thanks, James On May 9, 2007, at 10:47 AM, Daniel Gaffney wrote:
4) In the middle an interface will appear that looks like the Table Browser. You can then select the Human Mar 2006 (hg18) assembly. Select Comparative Genomics as the group, 28-way Cons as the track and "multiz28wayAnno" as the table. Make sure that genome is selected as the region. Then select MAF as the output type. 5) Check the box that says "Send output to Galaxy". Press "get output" button and the "Send query to Galaxy" button. (Up to this point can also be done in the Table Browser on genome-test). Getting the MAF output seems to be rather slow.