[BioC] EasyRNASeq - gff file is not recognized

[Nicolas Delhomme]

Dear Gabriela,

Given that error:

> 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?


your gff3 appears not to contain a header.

Add the following line:

##gff-version 3

to the beginning of your gff3 file and that should solve the problem.

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On 6 Mar 2013, at 10:57, Gabriela [guest] wrote:

> 
> Hello, 
> 
> 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,
> 
> Gabriela
> 
> -- 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,  :
>   
>> 
> 
> 
> 
> 
> 
> 
> 
> 
>> 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] 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
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.