[BioC] regarding makeTranscriptDbFromGFF

[Steve Lianoglou]

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