Jim Kent informs me that you can do it this way:
For the command line you can achieve this just by swapping target and
query.
Your 32bp sequences would become tiny targets,
you would need -t=dnax -q=prot.
Happy BLAT-TING!
-Galt
Galt Barber wrote:
> Hi, Fabio!
>
> Here are the type combinations supported by blat from blat.c:
>
> if (bothSimpleNuc || bothSimpleProt)
> {
> [...]
> }
> else if (tType == gftDnaX && qType == gftProt)
> {
> [...]
> }
> else if (tType == gftDnaX && (qType == gftDnaX || qType == gftRnaX))
> {
> [...]
> }
> else
> {
> errAbort("Unrecognized combination of target and query types\n");
>
>
>
> What you would love to see and what is missing is this line:
>
> else if (tType == gftProt && (qType == gftDnaX || qType == gftRnaX))
> {
> [...]
> }
> But this combination is not supported by BLAT.
> Perhaps Jim Kent felt that BLAST already did this well enough
> and did not choose to support this.
>
> You could try converting your reads into 3 frames of protein
> and then using blat -prot.
>
> By the way, if you are specifying -out-blast8 then you wouldn't
> typically give your output file name the extension .psl.
>
> The results you got when using -prot on a dna query
> are invalid. Do not use them.
>
> -Galt
>
> Fabio Gori wrote:
>> Hi,
>>
>> Sice my reads are just 32bp long, I am trying to use blat instead of blastx
>> to
>> map them into proteins.
>> I am trying to run
>> blat nr.fa seqsaglobus.fa ris2.psl -t=prot -q=dnax -tileSize=8 -stepSize=3
>> -
>> fine -repMatch=1000000 -out=blast8
>>
>> But I got the message:
>> d and q must both be either protein or dna
>>
>> I tried with
>> -t=prot -q=prot
>> and I get some results, but it should not work because seqsaglobus.fa is
>> made
>> by nucleotides.
>>
>> Can you explain me what happens?
>>
>> Thank you,
>>
>> Fabio
>>
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