Re: [Transdecoder-users] TransDecoder

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

Hi Suhaila,

It appears that our gtf-to-gff3 converter isn't compatible with the unknown
strand '.' designation and simply converts them all to '-'. So, for now,
the cufflinks compatibility is restricted to using strand-specific rna-seq,
where all transcripts have a defined orientation.  We'll aim to address
this in a future release.

best,

~brian


On Fri, Oct 3, 2014 at 2:59 AM, Suhaila Sulaiman <
suh...@gm...> wrote:

> Hi Brian,
>
> Good then. I've tried using cufflinks output (.gtf) and convert to gff3.
> In gtf file, the strand column show a '.' there for all of the transcripts.
> When I converted it to gff3, most of them show '-' in strand column. How
> does the script know which strand the transcripts in? Can you hel me on
> that?
>
> Regards,
>
>
>