[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)
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
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