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
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
For 1500 intervals this shouldn't take more than a minute or so. Let
me know how it goes.
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.
Comparative Genomics as the group, 28-way Cons as the track and
"multiz28wayAnno" as the table. Make sure that genome is selected
region. Then select MAF as the output type.
5) Check the box that says "Send output to Galaxy". Press "get
button and the "Send query to Galaxy" button. (Up to this point can
be done in the Table Browser on genome-test). Getting the MAF output
seems to be rather slow.