[Genome] Qs and comments about Table Browser and running Blat locally

[Iris Vargas Jentzsch]

Dear UCSC team,

 

First of all thanks so much for the wonderful job you do with the genome browser; my PhD project would certainly move on very slowly without the tools and information you make available.

 

I would like to point out that a tool in the table browser seems not to work properly. When trying to do an intersection among two datasets using the option "Complement before intersection/union" I get the same result as without ticking the box. As I understand it if I Intersect the complement of a set of intervals with any other table I should get a list of features that do not intersect with the first ones. Could you please check that or let me know if I'm interpreting it wrong?

 

Another comment: It would be very useful to have an additional button in the Table Browser section to manage custom tracks directly from there. The way it works now it is necessary to load the genome browser first in order to click on the button to manage the custom tracks. Since the genome browser page has much more elements to load it needs relatively longer to load, even though this is not relevant when we only want to load a custom track.

 

And finally, I have a question about Blat. I would like to install Blat to run locally on 

a supercomputer to be able to compute whole genomic searches. I read in the paper that Blat is suitable for batch runs in one or more CPUs. Does this mean that Blat can be run in parallel?  More specifically; could you let me know where to find information about running Blat efficiently on more than one processor?

 

Thanks in advance for your help,

 

Iris





-- 
Iris M. Vargas Jentzsch
School of Biological Sciences
University of Canterbury
Private Bag 4800
Christchurch - New Zealand
Phone: +64 (0) 3 364 2987  (7048)