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
