Error in export.gff from rtracklayer
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Entering edit mode
Jon Bråte ▴ 240
@jon-brate-6263
Last seen 16 months ago
Norway

Hi,

I imported a gtf-file using makeTxDbFromGFF() and made a GRangesList of introns by:

introns = intronsByTranscript(object, use.names=TRUE)

But I get an error trying to export the introns as gff/gtf file:

export.gff(introns, "introns.gff", format="gff")

Error in .local(x, ...) :
  Elements in a group must be on same sequence and strand

If I for instance extract genes the export works fine. How can the introns be on different strands/sequences when the genes are not? Btw, all the features in my imported gtf-file are on the same strand.

Thanks, Jon

 

Edit: I converted the introns object to a GRanges object and it seems to work...

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.18.4   rtracklayer_1.28.10    seqinr_3.1-3           ade4_1.7-2             Biostrings_2.36.4     
 [6] XVector_0.8.0          GenomicFeatures_1.20.5 AnnotationDbi_1.30.1   Biobase_2.28.0         GenomicRanges_1.20.8  
[11] GenomeInfoDb_1.4.3     IRanges_2.2.7          S4Vectors_0.6.6        BiocGenerics_0.14.0   

loaded via a namespace (and not attached):
 [1] zlibbioc_1.14.0         GenomicAlignments_1.4.1 BiocParallel_1.2.21     tools_3.2.1            
 [5] DBI_0.3.1               lambda.r_1.1.7          futile.logger_1.4.1     futile.options_1.0.0   
 [9] bitops_1.0-6            RCurl_1.95-4.7          biomaRt_2.24.1          RSQLite_1.0.0          
[13] Rsamtools_1.20.4        XML_3.98-1.3 
rtracklayer gff • 1.1k views
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Entering edit mode

Would help to get a hold of your actual data for reproducing this. But I will say that you probably want to output to "gff3" rather than "gff", which implies gff2. Note that exporting a GRangesList of introns that way will represent them as exons in the GFF3, which will be a bit strange. This could be made more flexible, if needed.

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