[Bioperl-l] low complexity filter in StandAloneBlastPlus

[Paul Cantalupo]

Hi Carne,

Take a look at the synopsis of
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods. I think you need to use
the method_args parameter:

 $result = $fac->blastn( -query => 'query_seqs.fas',
                         -outfile => 'query.bls',
                         *-method_args => [ '-dust' => 'no' ]* );


Best,

Paul

Paul Cantalupo
University of Pittsburgh


On Thu, Feb 13, 2014 at 4:43 PM, Carnë Draug <carandraug+dev at gmail.com>wrote:

> Hi
>
> I'm using Bio::Tools::Run::StandAloneBlastPlus and it's working
> perfectly. I'm getting exactly the same results as if running it on
> NCBI's server with default values.
>
> However, I want to remove the low complexity filter but can't see this
> mentioned anywhere. How can I do this in StandAloneBlastPlus?
>
> Thanks in advance,
> Carnë
>
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