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
