[Genome] BLAT Table Function

[Archana Thakkapallayil]

Hello Carsten,

I assume you are trying to use the intersection tool in the Table Browser.

However, the Table Browser does not have a "join" function that will 
give you the name and position of your element to a corresponding 
element in another track.The results only give the items and their 
positions from the first table that you selected (not the one that you 
selected to intersect with) that intersect with the second table, so you 
are unable to get both sets of information in the output.

There is another tool run by Penn State that works in conjunction with 
the UCSC Genome Browser that can do joins.  It is called "Galaxy", and 
it is located here:

http://main.g2.bx.psu.edu/

Also, we do provide a link to 'Galaxy' from our Table Browser, by 
checking the box 'Send output to Galaxy'. This displays results of query 
in Galaxy, a framework for interactive genome analysis.

Galaxy has a tool to "Join the intervals of two queries side-by-side" 
that you can use.The "join intervals" function is under the "Operate on 
genomic intervals" section on the left-hand side.

I hope this information is helpful to you. If this does not answer your 
question, please don't hesitate to write back to the list.

Regards,

Archana
UCSC Genome Bioinformatics Group

We invite you to give us your feedback on the UCSC Genome Browser 
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177


Carsten Lederer wrote:
> Dear UCSC Genome Team. 
>
> We find the BLAT table function tremendously powerful in retrieving information on genes adjacent to our viral vector integrations in the human genome. On the downside, when using the position of our integration (i.e. a 60 kb range centred around that position), we cannot submit additional identifiers to then correlate the output with the information we already have for our integration sites. 
> For position information it is already possible to submit a fourth field, but that field is then not displayed in the output table. Ideally, an input format like "chr7:73739410-73799410 Site0001" would result in an output like "Site0001 uc003uat.1 ..." that would allow us to use e.g. the Excel Vlookup function for annotation. At present we use the positional information on the chromosome to match BLAT Table outputs with our own data, which is somewhat awkward (for your info, we sort positions in ascending order and use Vlookup with the range_lookup set to "True") and leads to errors if two integrations are close to one another. 
>
> Is there a function or check box I have overlooked? Otherwise, would it be possible to offer the option of displaying the fourth (ID) field in the output table? Or what other solution to our problem (more elegant than our current work-around) would you suggest? 
>
> I would be grateful for your feedback or input. Keep up the good work, 
> Carsten Lederer    
>
> Carsten Lederer, PhD
> --------------------
> Telethon Institute of Gene Therapy
> Fondazione San Raffaele del Monte Tabor
> Via Olgettina 58
> 20132 Milan
> Italy
> --------------------
> Phone 0039-02-26434707
> Fax   0039-02-26434668
> --------------------
> Carsten at inbox.com
> C.Lederer at hsr.it
>
> ____________________________________________________________
> GET FREE 5GB EMAIL - Check out spam free email with many cool features!
> Visit http://www.inbox.com/email to find out more!
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>