[Bioperl-l] script to calculate percentage identity for BLAT psl
gopu_36 at yahoo.com
Sat Mar 14 22:38:31 EDT 2009
Thanks for your help.
I did try as below for testing purpose:
blat database.fa query.fa output.psl
blat database.fa query.fa output.blast
Both the results looks the same and the output.blast also lokks lo=ike
normal psl format. As I have always used .psl format, I am not sure what the
problem while getting the blast like output? Could you please let me know?
Thanks you so much.
Jason Stajich-3 wrote:
> well you could just output it in blast9 output and then the 3rd column
> is percent identity.
> On Mar 14, 2009, at 6:04 PM, gopu_36 wrote:
>> Please let me know whether any other way of calculating the precentage
>> identity for commandline BLAT results? . Thanks.
>> gopu_36 wrote:
>>> I did go through FAQ from BLAT on how to calculate the precentage
>>> from http://genome.ucsc.edu/FAQ/FAQblat#blat4
>>> As a new comer, I don;t usederstand on how to implement this.
>>> Please let
>>> me know how to plugin the script for my output.psl file. Please let
>>> know. It would be of great help.
>>> Thanks and Regards.
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> Jason Stajich
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