Hi Peng, BAM format has the same mismatch/gap display features. For more information, please see: http://genome.ucsc.edu/goldenPath/help/bam.html
Contact us again at [email protected] if you have additional questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 11/8/2011 7:06 AM, Peng Yu wrote: > 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 >>> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
