Dario Strbenac | 8 May 07:00 2013
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makeTranscriptDbFromGFF for Unstranded Transcripts

Hello,

I have assembled transcripts based on unstranded RNA-seq data. It's not the ideal experimental design, of
course. Is it not possible to make a TranscriptDb object from this ?

makeTranscriptDbFromGFF("transcripts.gtf", format = "gtf", exonRankAttributeName = "exon_number")
extracting transcript information
Estimating transcript ranges.
Extracting gene IDs
Processing splicing information for gtf file.
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
Error in .normargTranscripts(transcripts) : 
  values in 'transcripts$tx_strand' must be "+" or "-"

R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
GenomicFeatures_1.12.1

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia

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