Hii...

Ok, i got it. Actually i was thinking warning message also an error and yes
its a fuctional txdb and trying so many fuctions and it works.If i want to
add chromosome information then what should i do. I am trying but it did
not work.
I am learning these new things so apologize for asking very basic question.

Thanks for your response.




On Thu, Sep 26, 2013 at 6:59 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> If your last attempt didn't work (I'll keep that portion of your email
> quoted below) there should be an error that was reported, but I only
> see warnings.
>
> Are there errors that come up after this?
>
> > Finally i remove dataSource, chromoinfo but again failed.
> >
> > txdb <- makeTranscriptDbFromGFF(file =
> > "all.gff3",format="gff",species="oryza sativa")
> > extracting transcript information
> > Extracting gene IDs
> > extracting transcript information
> > Processing splicing information for gff3 file.
> > Deducing exon rank from relative coordinates provided
> > Prepare the 'metadata' data frame ... metadata: OK
> > Now generating chrominfo from available sequence names. No chromosome
> > length information is available.
> > Warning messages:
> > 1: In .deduceExonRankings(exs, format = "gff") :
> >   Infering Exon Rankings.  If this is not what you expected, then please
> be
> > sure that you have provided a valid attribute for exonRankAttributeName
> > 2: In matchCircularity(chroms, circ_seqs) :
> >   None of the strings in your circ_seqs argument match your seqnames.
>
> Is there something more that is outputted that's missing from your
> email? The fact that there are no errors reported suggests that you
> should now have a functional(?) `txdb` object ... do you?
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

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