[BioC] makeTranscriptDbFromGFF Error for UCSC GTF File

Dario Strbenac dstr7320 at uni.sydney.edu.au
Wed Jul 2 09:00:20 CEST 2014


Hello,

I used :

> system.time(hg19 <- makeTranscriptDbFromGFF("/home/dario/data/Annotation/hg19.gtf", format = "gtf"))
Error in .parse_attrCol(attrCol, file, colnames) : 
  Some attributes do not conform to 'tag value' format
Timing stopped at: 15.605 0.296 16.07 

I downloaded the GTF file from UCSC Table Browser. The table's name was refGene. To me, it seems that the attributes are fine :

> hg19table <- read.table("/home/dario/data/Annotation/hg19.gtf", sep = '\t', stringsAsFactors=FALSE)
> table(sapply(strsplit(hg19table[, 9], ' '), length))

     4 
967118

I have R version 3.1.0 (2014-04-10) and GenomicFeatures 1.16.2

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


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