[BioC] [devteam-bioc] GenomicFeatures support for UCSC Microbial Genome Browser

Hervé Pagès hpages at fhcrc.org
Thu Jan 16 00:09:40 CET 2014

Hi Sonia,

Might just be easier to download the GFF file directly from NCBI
and turn it into a TranscriptDb object with makeTranscriptDbFromGFF().

In 5 steps:

   1. Pick-up your bacteria from this index:


      For example Campylobacter_jejuni_NCTC_11168 in your case.

   2. Click on it.

   3. Download the GFF file (HE978252.gff in this case).

   4. Start R, load the GenomicFeatures package and run
      makeTranscriptDbFromGFF() on the GFF file.
      If you run into problems, ?makeTranscriptDbFromGFF is your

   5. Let us know how it goes.

Note that gene models for bacteria are so simple that putting them in
a TranscriptDb object feels a little bit overkill but is sometimes
needed for interoperability with some of the tools in BioC.


On 01/11/2014 03:33 AM, Maintainer wrote:
> Hi,
> I tried using the GenomicFeatures package (R package) to get gene information for Salmonella enterica serovar Typhimurium SL1344 (uid86645) and Campylobacter jejuni (NCTC1168) from the UCSC genome browser,but discovered that UCSC genome browser did not have the two organisms; however, the two organisms are hosted in UCSC Microbial Genome Browser. I wonder if there is any plan to support UCSC Microbial Genome Browser in the nearest future.
> Thanks
>   -- output of sessionInfo():
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
>   [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
>   [1] rtracklayer_1.20.4     GenomicRanges_1.12.5   IRanges_1.18.2         lumiMouseAll.db_1.20.0 org.Mm.eg.db_2.9.0     RSQLite_0.11.4         DBI_0.2-7
>   [8] annotate_1.38.0        AnnotationDbi_1.22.6   limma_3.16.7           lumi_2.12.0            gplots_2.12.1          DESeq_1.12.0           lattice_0.20-24
> [15] locfit_1.5-9.1         Biobase_2.20.1         BiocGenerics_0.6.0     doMC_1.3.1             iterators_1.0.6        foreach_1.4.1
> loaded via a namespace (and not attached):
>   [1] affy_1.38.1           affyio_1.28.0         beanplot_1.1          BiocInstaller_1.10.3  Biostrings_2.28.0     bitops_1.0-6          BSgenome_1.28.0
>   [8] caTools_1.16          codetools_0.2-8       colorspace_1.2-2      compiler_3.0.2        gdata_2.13.2          genefilter_1.42.0     geneplotter_1.38.0
> [15] grid_3.0.2            gtools_3.1.0          illuminaio_0.2.0      KernSmooth_2.23-10    MASS_7.3-29           Matrix_1.1-1.1        matrixStats_0.8.5
> [22] mclust_4.2            methylumi_2.6.1       mgcv_1.7-27           minfi_1.6.0           multtest_2.16.0       nleqslv_2.0           nlme_3.1-113
> [29] nor1mix_1.1-4         preprocessCore_1.22.0 RColorBrewer_1.0-5    RCurl_1.95-4.1        reshape_0.8.4         R.methodsS3_1.5.2     Rsamtools_1.12.4
> [36] siggenes_1.34.0       splines_3.0.2         stats4_3.0.2          survival_2.37-4       tools_3.0.2           XML_3.98-1.1          xtable_1.7-1
> [43] zlibbioc_1.6.0
> --
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
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