Re: [Transdecoder-users] question about Transdecoder

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

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