[BioC] EasyRNASeq - gff file is not recognized

Gabriela [guest] guest at bioconductor.org
Wed Mar 6 10:57:19 CET 2013


I am trying to generate a table of gene counts to use later with Deseq. However, I got an error message that the maize gff file that I am using is wrong. I downloaded this file directly from the plant ensembl website. 

I have to mention that I used a .gff file and a .gff3, and with both I have the same issue. Any hint in how to solve my problem.

Many thanks for your help in advance,


 -- output of sessionInfo(): 

> genes_FGS1 <- easyRNASeq(filesDirectory="/projects/EASYRNASeq/",
+  gapped=F,
+ validity.check=TRUE,
+ chr.map=chr.map,
+ organism="custom",
+ annotationMethod="gff",
+ annotationFile="/projects/ZmB73_5b_FGS.gff3",
+ count="genes",
+ filenames=files,
+ summarization="geneModels",
+ outputFormat="RNAseq")
Checking arguments...
Fetching annotations...
Error in .readGffGtf(filename = filename, ignoreWarnings = ignoreWarnings,  :
  Your file: /projects/ZmB73_5b_FGS.gff3 does not contain a gff header: '##gff-version 3' as first line. Is that really a gff3 file?

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

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
 [1] VennDiagram_1.5.1      easyRNASeq_1.4.2       ShortRead_1.16.1
 [4] latticeExtra_0.6-24    RColorBrewer_1.0-5     BSgenome_1.26.1
 [7] biomaRt_2.14.0         genomeIntervals_1.14.0 intervals_0.13.3
[10] Rsamtools_1.10.1       Biostrings_2.26.2      GenomicRanges_1.10.4
[13] IRanges_1.16.4         edgeR_3.0.2            limma_3.14.1
[16] pasilla_0.2.13         DESeq_1.10.1           lattice_0.20-10
[19] locfit_1.5-8           DEXSeq_1.2.1           Biobase_2.18.0
[22] BiocGenerics_0.4.0     pasillaBamSubset_0.0.2

loaded via a namespace (and not attached):
 [1] annotate_1.34.1      AnnotationDbi_1.18.1 bitops_1.0-4.2
 [4] DBI_0.2-5            genefilter_1.38.0    geneplotter_1.34.0
 [7] hwriter_1.3          plyr_1.7.1           RCurl_1.91-1
[10] RSQLite_0.11.1       splines_2.15.2       statmod_1.4.15
[13] stats4_2.15.2        stringr_0.6.1        survival_2.36-14
[16] tools_2.15.2         XML_3.9-4            xtable_1.7-0
[19] zlibbioc_1.4.0

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