Hi,
GenomicFeatures 0.4.5 (in devel) now supports the following databases
in addition to ensembl: bacterial_mart_4, fungal_mart_4, metazoa_mart_4,
plant_mart_4, protist_mart_4 and Ensembl56.
Note that only ensembl and Ensembl56 have CDS information.
For example, for Arabidopsis, you'll get a warning that the
CDS information is missing:
> txdb <- makeTranscriptDbFromBiomart("plant_mart_4",
"athaliana_eg_gene")
Warning message:
In .normargSplicings(splicings, unique_tx_ids) :
no CDS information for this TranscriptDb object
> txdb
TranscriptDb object:
| Db type: TranscriptDb
| Data source: BioMart
| BioMart database: plant_mart_4
| BioMart dataset: athaliana_eg_gene
| BioMart dataset description: Arabidopsis thaliana genes (TAIR9)
| BioMart dataset version: TAIR9
| Full dataset: yes
| transcript_nrow: 39640
| exon_nrow: 176581
| cds_nrow: 0
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2010-03-22 23:32:17 -0700 (Mon, 22 Mar 2010)
| GenomicFeatures version at creation time: 0.4.5
| RSQLite version at creation time: 0.8-4
Thanks for your feedback. Let us know if you find any other problem with
the GenomicFeaturess package.
Cheers,
H.
[email protected] wrote:
Dear bioc-sig-sequencing,
I would like to annotate chip-seq peaks for the arabidopsis genome. I note that the
GenomicFeatures vignette, section 2.7.3 of the pdf file "Making & using TranscriptDb
objects", is suggested for Chip-seq experiments.
Trying the example in section 2.7.3 of the vignette (but substituting
arabidopsis for mouse) resulted in an message that only the 'ensembl' database
is now supported.
In what follows, have I selected the appropriate biomart database and dataset
for my purpose? If so, when might GenomicFeatures support them? If support
will not be soon, can someone suggest an alternative approach for my task?
mart4_at_eg_gene <-
+ makeTranscriptDbFromBiomart(biomart = "plant_mart_4",
+ dataset = "athaliana_eg_gene")
Error in makeTranscriptDbFromBiomart(biomart = "plant_mart_4", dataset =
"athaliana_eg_gene") :
only 'biomart="ensembl"' is supported for now
sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-18 r51318)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.3.4 GenomicFeatures_0.4.2 BSgenome_1.15.15
[4] Biostrings_2.15.24 GenomicRanges_0.0.4 IRanges_1.5.63
loaded via a namespace (and not attached):
[1] Biobase_2.7.5 DBI_0.2-5 RCurl_1.3-1 RSQLite_0.8-4
[5] rtracklayer_1.7.11 tools_2.11.0 XML_2.6-0
Thanks,
P. Terry
[email protected]
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: [email protected]
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Fax: (206) 667-1319
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