[Genome] BLAT Table Function

[Carsten Lederer]

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
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Telethon Institute of Gene Therapy
Fondazione San Raffaele del Monte Tabor
Via Olgettina 58
20132 Milan
Italy
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Phone 0039-02-26434707
Fax   0039-02-26434668
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Carsten at inbox.com
C.Lederer at hsr.it

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