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problems running DEseq2

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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.

DESeq2 DESeq2 • 808 views

ADD COMMENT • link updated 9.8 years ago by Michael Love 42k • written 9.8 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2014-08-11

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] <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) > > 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.