Cook, Malcolm | 1 Aug 17:12 2006

Re: Getting sequences by base pair locations

Yuval,

Glad to help.  Given that you are not running blat suite locally, but at
ucsc, you should try this approach:

upload/paste your blat results (in blat's native output format, psl) as
a custom track in the genome browser, named, say, myhumanhits
(i.e. just give the blat results a new first line like: `track
name="myhumanhits" description="myhumanhits from my favorite human
genes" visibility=2`)
then goto the table browser and configure it 
	group = 'custom tracks'
	track = 'myhumanhits'
	retion = genome
	output format = sequence
	output file = myhumanhits.fasta

submit it

When prompted, Save the myhumanhits.fasta to your computer and take it
from there.

I'm not sure how many hits this will work for, but i just did this on a
small track and it works just fine.  Only problem, the first word in the
fasta defline is always the same for all sequences.  You'll have to
'uniqify' these names somehow probably (depedning of course on your
application).

Let us know & Good luck & ask for good email support on ucsc genome
browser subscribe to
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Gmane