Hi, I have run the function,makeTranscriptDbFromGFF, of the GenomicFeatures package with the simplest way ???txdb <- makeTranscriptDbFromGFF(file = "Vitis_vinifera.IGGP_12x.gtf", format = "gtf")???or other complicate way and always got the following errors: 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. I got the gtf file of vitis vinefera from here: http://plants.ensembl.org/info/data/ftp/index.html. And I also tried the instructions of makeTranscriptDbFromGFF on the website as the following: gtfFile <- system.file("extdata","Aedes_aegypti.partial.gtf", package="GenomicFeatures") txdb <- makeTranscriptDbFromGFF(file = gtfFile, format= "gtf"). Unfortunately, I got the same error as the vitis gtf file was used. So I am confused. Why did the errors happen even if I use the sample file? Thank you! -- output of sessionInfo(): output txdb <- makeTranscriptDbFromGFF(file = "Vitis_vinifera.IGGP_12x.gtf", format = "gtf") 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. 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. > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 [2] LC_CTYPE=Chinese (Simplified)_China.936 [3] LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_China.936 attached base packages: [1] parallel stats graphics grDevices utils datasets [7] methods base other attached packages: [1] GenomicFeatures_1.14.3 AnnotationDbi_1.24.0 [3] Biobase_2.22.0 GenomicRanges_1.14.4 [5] XVector_0.2.0 IRanges_1.20.7 [7] BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 [4] BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1 [7] Rsamtools_1.14.3 RSQLite_0.11.4 rtracklayer_1.22.4 [10] stats4_3.0.2 tools_3.0.2 XML_3.98-1.1 [13] zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Murli, I just now saw that your email went to not only my inbox, but also to the bioconductor mailing list as well. I will now answer it here so that others who may have similar questions can benefit: Those are not actually errors. They are warnings. An error means something severe went wrong and the code cannot (or should not) continue. A warning means you should look at this message in case this detail might affect you. The 1st of these warning messages is telling you that your file did not contain exon ranking information (and so the order is being inferred by the order that the exons are present in the source file). You may or may not feel comfortable with that inference. Frankly, it depends on the file (and the species of organism) whether or not its a fair thing to assume and we expect that you will know whether or not you need to worry about it. The other warning says that your the code was unable to guess about which (if any) of your chromosomes were circular. Whether any of that is a problem or not will entirely depend on you and what you want (and what you want to do next). It's not possible for us to know whether or not these circumstances are a problem for you or not, so we issue a warning (instead of an error). Marc On 03/12/2014 02:27 PM, Maintainer wrote: > Hi, > I have run the function,makeTranscriptDbFromGFF, of the GenomicFeatures package with the simplest way ï¼^txdb <- makeTranscriptDbFromGFF(file = "Vitis_vinifera.IGGP_12x.gtf", format = "gtf")ï¼0/00or other complicate way and always got the following errors: > 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. > I got the gtf file of vitis vinefera from here: > http://plants.ensembl.org/info/data/ftp/index.html. > > And I also tried the instructions of makeTranscriptDbFromGFF on the website as the following: > gtfFile <- system.file("extdata","Aedes_aegypti.partial.gtf", package="GenomicFeatures") > txdb <- makeTranscriptDbFromGFF(file = gtfFile, format= "gtf"). > Unfortunately, I got the same error as the vitis gtf file was used. > So I am confused. Why did the errors happen even if I use the sample file? > Thank you! > > -- output of sessionInfo(): > > output > txdb <- makeTranscriptDbFromGFF(file = "Vitis_vinifera.IGGP_12x.gtf", format = "gtf") > 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. > 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. > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Chinese (Simplified)_China.936 > [2] LC_CTYPE=Chinese (Simplified)_China.936 > [3] LC_MONETARY=Chinese (Simplified)_China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese (Simplified)_China.936 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > [7] methods base > > other attached packages: > [1] GenomicFeatures_1.14.3 AnnotationDbi_1.24.0 > [3] Biobase_2.22.0 GenomicRanges_1.14.4 > [5] XVector_0.2.0 IRanges_1.20.7 > [7] BiocGenerics_0.8.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 > [4] BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1 > [7] Rsamtools_1.14.3 RSQLite_0.11.4 rtracklayer_1.22.4 > [10] stats4_3.0.2 tools_3.0.2 XML_3.98-1.1 > [13] zlibbioc_1.8.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave@lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc [[alternative HTML version deleted]]