[BioC] problems running DEseq2
michaelisaiahlove at gmail.com
Mon Aug 11 21:41:56 CEST 2014
Here's some information from a previous thread:
the brief version: not all GTF files contain sufficient/correct
information to create a txdb. the good news is that you can most
likely use the prebuilt txdb for the known genes track referenced in
On Mon, Aug 11, 2014 at 3:35 PM, Julian Rozenberg [guest]
<guest at bioconductor.org> wrote:
> rying to run deseq2.
> I am trying to use ref seq genes from UCSC to build a set of reference coordinates according to you manual.Refseq genes are downloaded from UCSC in .GTF format from gene and gene prediction group.
>>hse <- makeTranscriptDbFromGFF( "/proj/macklab/projects/JR/RNA/refGene.gtf", format="gtf" )
> Error in .parse_attrCol(attrCol, file, colnames) :
> Some attributes do not conform to 'tag value' format
> Could you suggest how to proceed.
> Thank you very much in advance for you help.
> -- output of sessionInfo():
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>  LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
>  LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
>  LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
>  LC_PAPER=C LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
> attached base packages:
>  parallel stats graphics grDevices utils datasets methods
>  base
> other attached packages:
>  GenomicFeatures_1.12.1 AnnotationDbi_1.22.5 Biobase_2.20.1
>  GenomicRanges_1.12.3 IRanges_1.20.7 BiocGenerics_0.8.0
>  knitr_1.5 BiocInstaller_1.12.1
> loaded via a namespace (and not attached):
>  biomaRt_2.16.0 Biostrings_2.30.1 bitops_1.0-6 BSgenome_1.28.0
>  DBI_0.2-7 evaluate_0.5.1 formatR_0.10 RCurl_1.95-4.1
>  Rsamtools_1.12.3 RSQLite_0.11.4 rtracklayer_1.20.2 stats4_3.0.1
>  stringr_0.6.2 tools_3.0.1 XML_3.96-1.1 XVector_0.2.0
>  zlibbioc_1.6.0
> Sent via the guest posting facility at bioconductor.org.
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