Hello

I am creating transcriptDb object from GFF file using
maketranscriptDbFromGFF. I have sequencing data and mapped this data on
rice genome using tophat now i want to count the overlaps
of my genomic alignments with genes but when i ran it :


txdb <- makeTranscriptDbFromGFF(file = "all.gff3",format="gff",dataSource="
ftp://ftp.plantbiology.msu.edu",exonRankAttributeName="exon_number",species="oryza
sativa")
Error in DataFrame(...) : different row counts implied by arguments

and when i remove dataSource then again got the same error.


txdb <- makeTranscriptDbFromGFF(file = "all.gff3", format=
"gff",exonRankAttributeName= "exon_number",chrominfo =
"chrominfo",species="oryza sativa")
Error in DataFrame(...) : different row counts implied by arguments

Finally i remove dataSource, chromoinfo but again failed.

txdb <- makeTranscriptDbFromGFF(file =
"all.gff3",format="gff",species="oryza sativa")
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 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.
Warning messages:
1: In .deduceExonRankings(exs, format = "gff") :
  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.

actually i am trying so many times but everytime i got error.

please tell me how to solve this problem.



sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252
 LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C                   LC_TIME=English_India.1252

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

other attached packages:
[1] GenomicFeatures_1.12.4 AnnotationDbi_1.22.6   Biobase_2.20.1
GenomicRanges_1.12.5   IRanges_1.18.4
[6] BiocGenerics_0.6.0     BiocInstaller_1.10.3

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0     Biostrings_2.28.0  bitops_1.0-6
BSgenome_1.28.0    DBI_0.2-7          RCurl_1.95-4.1
 [7] Rsamtools_1.12.4   RSQLite_0.11.4     rtracklayer_1.20.4 stats4_3.0.1
      tools_3.0.1        XML_3.98-1.1
[13] zlibbioc_1.6.0




regards

Deepika

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