problems running DEseq2
"Julian Rozenberg [guest]" <[email protected]>
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <[email protected]> |
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. _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor