Re: [Transdecoder-users] question about Transdecoder

[Brian H. <bh...@br...>]

If you use the -S parameter, then only the top strand will be examined. If
you know ahead of time that the transcript sequence is
reverse-complemented, then you should reverse-complement the sequence
before providing it to transdecoder with the -S option.

best,

~brian



On Tue, Jul 29, 2014 at 2:33 AM, 130...@pk... <
130...@pk...> wrote:

>  So, if a transcript is labeled "-" and we know the sense strand is
> negative，then Transdecoder will find the CDS in "-" strand or "+" strand
> with the option "-S" ?
>
>
> ------------------------------
>  130...@pk...
>
>  *From:* Brian Haas <bh...@br...>
> *Date:* 2014-07-24 19:50
> *To:* 130...@pk...
> *CC:* transdecoder-users <tra...@li...>
> *Subject:* Re: [Transdecoder-users] question about Transdecoder
>  Hi,
>
> The top strand is the sense strand in the case that you have all the input
> transcripts already oriented in their transcribed orientation (ie. from
> using strand-specific rna-seq assembly).
>
> We don't have utilities included to select the single 'best' ORF per
> transcript.  All likely coding regions are reported.
>
> best,
>
> ~brian
>
>
> On Wed, Jul 23, 2014 at 11:16 PM, 130...@pk... <
> 130...@pk...> wrote:
>
>>  Hi, I am glad to write to you！
>> I want to use Transdecoder to find out the ORF. But I have two question:
>> 1. what does the "top strand" mean? "If the transcripts are oriented
>> according to the sense strand, then include the -S flag to examine only the
>> top strand. "
>> 2. If I only want to find out the longest ORF in the DNA sequense, what
>> should I do ?
>>
>> Thanks!
>>
>>
>> ------------------------------
>>   130...@pk...
>>
>>
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>>
>
>
> --
> --
> Brian J. Haas
> The Broad Institute
> http://broad.mit.edu/~bhaas
>
>
>



-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas