hello guys,
i am having trouble to build a txdb object for S.lycopersicum
GTF file link :http://www.ncbi.nlm.nih.gov/genome/?term=solanum+lycopersicum
the command i used :
gtffile <- file.path("~/Desktop/s.lyco gff/new one/GCF_000188115.3_SL2.50_genomic.gff")
txdb <- makeTxDbFromGFF(gtffile, format= "gtf",circ_seqs=character())
ERROR:
Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Warning message: In .local(con, format, text, ...) : gff-version directive indicates version is 3, not 2 Error in ID[gene_IDX] %in% unlist(Parent[exon_with_gene_parent_IDX], use.names = FALSE) : error in evaluating the argument 'table' in selecting a method for function '%in%': Error in unlist(Parent[exon_with_gene_parent_IDX], use.names = FALSE) : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : subscript contains NAs or out-of-bounds indices
> sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.3 LTS locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] TxDb.Athaliana.BioMart.plantsmart28_3.2.2 [2] BiocInstaller_1.20.1 [3] GenomicFeatures_1.22.8 [4] AnnotationDbi_1.32.3 [5] Biobase_2.30.0 [6] GenomicRanges_1.22.3 [7] GenomeInfoDb_1.6.1 [8] IRanges_2.4.6 [9] S4Vectors_0.8.7 [10] BiocGenerics_0.16.1 loaded via a namespace (and not attached): [1] XVector_0.10.0 zlibbioc_1.16.0 [3] GenomicAlignments_1.6.3 BiocParallel_1.4.3 [5] tools_3.2.3 SummarizedExperiment_1.0.2 [7] DBI_0.3.1 lambda.r_1.1.7 [9] futile.logger_1.4.1 rtracklayer_1.30.1 [11] futile.options_1.0.0 bitops_1.0-6 [13] RCurl_1.95-4.7 biomaRt_2.26.1 [15] RSQLite_1.0.0 Biostrings_2.38.3 [17] Rsamtools_1.22.0 XML_3.98-1.3
hi michael , thx for the reply, however i got another error trying to run it like this
Looks like a case of trans-splicing. That does not appear to be supported by GenomicFeatures yet. Herve?