[Bioperl-l] script to calculate percentage identity for BLAT psl

gopu_36 gopu_36 at yahoo.com
Sat Mar 14 23:33:01 EDT 2009


Yes Jason, Thanks and I did it using -out=type. Thanks.

Jason Stajich-3 wrote:
> 
> you should read the blat documentation - if you type blat alone on the  
> command-line or read any of the documentation UCSC provides for the  
> tool  it gives you lots of detailed information on how to run it. I  
> bet you can figure out how to specify a different output format based  
> on reading that documentation.
> 
> -jason
> On Mar 14, 2009, at 7:39 PM, gopu_36 at yahoo.com wrote:
> 
>> Hi Jason,
>> 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?
>> 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:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I did go through FAQ from BLAT on how to calculate the precentage
>>>>> identity
>>>>> 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
>>>>> me
>>>>> know. It would be of great help.
>>>>>
>>>>> Thanks and Regards.
>>>>>
>>>>
>>>> -- 
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>>>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>>>
>>>> _______________________________________________
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>>>
>>> Jason Stajich
>>> jason at bioperl.org
>>>
>>>
>>>
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>>> Bioperl-l at lists.open-bio.org
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>>>
>>>
>> Quoted from:
>> http://www.nabble.com/script-to-calculate-percentage-identity-for-BLAT-psl-tp22476983p22519116.html
>>
> 
> Jason Stajich
> jason at bioperl.org
> 
> 
> 
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> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

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