Hi Peng, Here is some additional information: we generally use "intron" lines (or gaps in the alignment) to show the direction of alignment by superposing ">>>>" (+ strand) or "<<<<<" (- strand) on the line between aligned blocks. When the entire alignment is one block with no gaps, there is no line on which to draw arrows. For some of our other tracks, we draw ">>>" on top of single-block alignments, but this capability is currently not enabled in BLAT results, sorry.
Until we can fix that, here is an admittedly hokey workaround. If your sequence is larger than a couple hundred bases, simply delete some sequence in the middle when pasting into the BLAT search page. That will create an alignment gap on which arrows will be drawn in the graphical display. Of course it will also affect the alignment process, so this may not be a good workaround for you, but thought I'd mention it. Hope that helps, and please contact us again if you have more questions, Angie ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Peng Yu" <[email protected]> > Cc: [email protected] > Sent: Monday, June 7, 2010 2:34:14 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] How to show blat sequence orientation in genome browser > > Hello, > > The display in the browser is always stranded for sequence alignments. > > Use the button "reverse" to switch strands (is under the main > display). > > Here is some help for interpreting the display clues for orientation > (arrows, lines, etc.). > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning > see Display conventions > > Hopefully this helps, > Jennifer > > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 6/7/10 1:52 PM, Peng Yu wrote: > > Hi, > > > > In the BLAT Search Results, it shows the strand information. But in > > the browser, it doesn't show the strand information graphically (I > > tried all the 4 display options, i.e, full...). Is it a way to show > > the strand information graphically in the genome browser? > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
