Re: problems running DEseq2

Thanks this is help full.

Julian Rozenberg, Ph.D.
Department of Pathology and Laboratory Medicine
The University of North Carolina
501 Brinkhous-Bullitt Bldg., CB#7525
Chapel Hill, NC 27599-7525
Tel: 954-478-4385
E-mail: [email protected]


2014-08-11 15:41 GMT-04:00 Michael Love <[email protected]>:

> 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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