The kent program 'pslPretty' will output the alignment picture of any psl file. It requires as input the query and target sequence files used in the alignment.
--Hiram Jennifer Jackson wrote: > Hi Peng, > > The sequences are the query and target as they exist in the sources. Use > the alignment information in the other psl data fields to determine > where any mismatches, gaps, etc. are present in the alignment. > > You could always output the actual alignments with BLAT if you want to > visualize the matches in detail. See the other "-out=type" options and > try a few to see which provides the best view for your uses. > > Thanks! > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 4/21/10 7:57 PM, Peng Yu wrote: >> On Wed, Apr 21, 2010 at 5:28 PM, Jennifer Jackson<[email protected]> wrote: >>> Hello Peng, >>> >>> pslx is the same as psl format with the sequence (query and target) >>> included. This is noted in the BLAT documentation: >>> >>> http://genome.ucsc.edu/goldenPath/help/blatSpec.html >>> >>> -out=type Controls output file format. Type is one of: >>> psl - Default. Tab separated format, no sequence >>> pslx - Tab separated format with sequence >>> etc .............. >> The word 'sequence' lacks clear definition. What sequence? Only the >> perfect matched would be shown? What about mismatch (in the middle and >> at the ends)? What about gaps? (These are what I mean by 'corner' >> cases. There may be other cases that I am not aware of.) >> >> I have tried some test cases. But since I am not able to dig into the >> source code of BLAT, I will not be able to enumerate all the possible >> cases. Could you or somebody who are familiar with BLAT show example >> output for each corner case? >> >>> FAQ for psl format: >>> http://genome.ucsc.edu/FAQ/FAQformat.html#format2 >>> >>> 21 columns for psl, 23 for pslx >>> >>> Hopefully this helps, >>> Jennifer >>> >>> --------------------------------- >>> Jennifer Jackson >>> UCSC Genome Informatics Group >>> http://genome.ucsc.edu/ >>> >>> On 4/21/10 8:50 AM, Peng Yu wrote: >>>> I could just guess what a field represents from the field name. But my >>>> guess may not correct for corner cases. Could you let me know where >>>> the description of the format is? Also, it seems that there are >>>> different number of fields above '----' and below it. Why? >>>> >>>> psLayout version 3 >>>> >>>> match mis- rep. N's Q gap Q gap T gap T gap strand Q >>>> Q Q >>>> Q T T T T block blockSizes >>>> qStarts tStarts >>>> match match count bases count bases >>>> name >>>> size start end name size start end >>>> count >>>> >>>> --------------------------------------------------------------------------------------------------------------------------------------------------------------- >>>> 24 0 0 0 0 0 0 0 + >>>> test_sequence 25 1 25 chr1 75 26 50 1 >>>> 24, 1, 26, ttgcaccggaaagtctgctccaga, >>>> ttgcaccggaaagtctgctccaga, _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
