 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
pterry@huskers.unl.edu

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