[BioC] problems running DEseq2

Julian Rozenberg [guest] guest at bioconductor.org
Mon Aug 11 21:35:44 CEST 2014

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)

 [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    

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