Hi,

I am trying to use the makeTranscriptDbFromGFF() function from the
GenomicFeatures R package to build a transcriptDB from a lncRNA gff file
available from http://www.lncipedia.org/download (version 2.1).

It gives this error when I run it:

$> lncRNADb <- makeTranscriptDbFromGFF(
'~/share/references/lncipedia_2_1.gtf', format = 'gtf', dataSource = '
http://www.lncipedia.org/', species = 'all' )

extracting transcript information
Estimating transcript ranges.
Extracting gene IDs
Processing splicing information for gtf 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.
Error in .normargSplicings(splicings, transcripts_tx_id) :
  'splicings$cds_start' must be an integer vector
In addition: Warning messages:
1: In .deduceExonRankings(exs, format = "gtf") :
  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.

Has anyone encountered this error before? Any help would be greatly
appreciated. Below is my sessionInfo(). Thanks,

Fong

---

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GenomicFeatures_1.10.1 AnnotationDbi_1.20.3   Biobase_2.18.0
[4] GenomicRanges_1.10.6   IRanges_1.16.4         BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.14.0     Biostrings_2.26.3  bitops_1.0-5
BSgenome_1.26.1
 [5] DBI_0.2-5          parallel_2.15.2    RCurl_1.95-3
Rsamtools_1.10.2
 [9] RSQLite_0.11.2     rtracklayer_1.18.2 stats4_2.15.2      tools_2.15.2

[13] XML_3.95-0.1       zlibbioc_1.4.0

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