Re: problems running DEseq2

hi Julian,

Here's some information from a previous thread:
https://stat.ethz.ch/pipermail/bioconductor/2014-July/060369.html

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
that thread.

Mike

On Mon, Aug 11, 2014 at 3:35 PM, Julian Rozenberg [guest]
<[email protected]> 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)
>
> locale:
>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>  [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>  [7] LC_PAPER=C                     LC_NAME=C
>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GenomicFeatures_1.12.1 AnnotationDbi_1.22.5   Biobase_2.20.1
> [4] GenomicRanges_1.12.3   IRanges_1.20.7         BiocGenerics_0.8.0
> [7] knitr_1.5              BiocInstaller_1.12.1
>
> loaded via a namespace (and not attached):
>  [1] biomaRt_2.16.0     Biostrings_2.30.1  bitops_1.0-6       BSgenome_1.28.0
>  [5] DBI_0.2-7          evaluate_0.5.1     formatR_0.10       RCurl_1.95-4.1
>  [9] Rsamtools_1.12.3   RSQLite_0.11.4     rtracklayer_1.20.2 stats4_3.0.1
> [13] stringr_0.6.2      tools_3.0.1        XML_3.96-1.1       XVector_0.2.0
> [17] zlibbioc_1.6.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.

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