Hi, Has there been any new development that export all the features available to blat for display to some kind of new file format? If not, may I suggest to the development term add one?
On Tue, Jun 22, 2010 at 1:39 PM, Mary Goldman <[email protected]> wrote: > Hi Peng, > > I'm sorry - I just realized the suggestion I emailed yesterday will not work > you. When users upload a psl as a custom track, we automatically convert it > to a bed file. However, even if you were able to make a custom track from a > psl, you would still not see all the alignment features that are displayed > by BLAT. I'm sorry, but you will have to use BLAT on the genome browser in > order to see all the alignment features. > > Best, > Mary > --------------------- > Mary Goldman > UCSC Bioinformatics Group > > On 6/21/10 5:23 PM, Mary Goldman wrote: >> >> Hi Peng, >> >> It is true that if you convert a psl to a bed or bigBED file you will >> end up losing some of the alignment information. Unfortunately, there is >> no "bigPsl" data format; if you have had trouble loading a large number >> of psl alignments as a custom track, you could try dividing them up by >> chromosome so you can load them in smaller batches. >> >> I hope this information is helpful. Please feel free to contact the >> mail list again if you require further assistance. >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> On 6/19/10 6:18 PM, Peng Yu wrote: >> >>> >>> Hi, >>> >>> I run blat on my own machine to get the psl files. Then I convert the >>> psl files to bed, then to bigBed, then show the bigBed file by custom >>> track. But the mismatch and overhang region can not be shown. By >>> "overhang region", I mean if there are some nucleotides at the ends >>> that are not mappable, they are indicated by a bar at the end in the >>> online version blat. >>> >>> Is there way a way to visualize the mismatches and overhang ends in >>> genome browsers? >>> >>> >>> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
