[Bioc-devel] makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)

Vincent Carey stvjc at channing.harvard.edu
Sun Nov 13 14:24:52 CET 2016

*(forgot to carbon list)*

*Did you not see a message like:*

*Import genomic features from the file as a GRanges object ... OK*

*Prepare the 'metadata' data frame ... OK*

*Make the TxDb object ... OK*

*Warning message:*

*In makeTxDbFromGRanges(gr, metadata = metadata) :*

*  The following transcripts were dropped because their exon ranks could*

*  not be inferred (either because the exons are not on the same*

*  chromosome/strand or because they are not separated by introns):*

*  NR_003254*

On Sun, Nov 13, 2016 at 5:25 AM, Marlin JL.M <marlin- at gmx.cn> wrote:

> Dear all,
> When trying to import the the GTF file downloaded from iGenome using
> makeTxDbFromGFF, I figured out that many genes are dropped silently,
> probably because those genes happens to have multiple chromosome
> locations in that GTF file.
> I have posted it at https://support.bioconductor.org/p/89401 with no
> reply yet. As I find it somehow a problem-causing bug, I decide to send
> the information here.
> Is there any suggested way to deal with the case?
> Best regards,
> Marlin
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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