[EMBOSS] extractfeat and "-join" option

[Andres Pinzon]

That's perfect,
thank you.

On Mon, Jun 22, 2009 at 11:44 AM, Peter Rice<pmr at ebi.ac.uk> wrote:
> Andres Pinzon wrote:'
>> Hi everyone,
>> The following line, should return a single fasta file with all the CDS
>> in a single sequence:
>>
>>  extractfeat environmental:DP000238 -type CDS -join stdout
>>
>> Instead it is returning each of them as a separate entry. Am I doing
>> something wrong?
>
> The -join option combines all exons for one CDS (so that it can be
> translated as a complete reading frame).
>
> It is not intended to join all CDSs into one.
>
> for environmental:DP000238 I get 10 CDSs with -join set and 52 (one per
> exon) without -join.
>
> Hope this helps,
>
> Peter
>
>



-- 
Andrés Pinzón
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