Dear bioc-sig-sequencing,
Previously, I tried the following with a UCSC available genome.
genetable<-read.table("celegans_chrIII.txt", header=T, sep="\t")
> promoter<-IRanges(start=genetable$txStart-1000*as.real(genetable$strand=="+"),
> width=1000)
It was suggested I might "check out the GenomicFeatures package, which has
utilities for working with a data.frame representation of the UCSC genes table.
For example, the 'transcripts' function will give you a set of regions,
including the promoters you're trying to generate."
I have a genome, arabidopsis, apparently not available at the UCSC database,
but rather from TAIR.
For this genome, might the GenomicFeatures pakage be similarly helpful? I
assume one might start with a file like TAIR9_GFF3_genes.gff from the TAIR
site? I note it has records for 'gene', 'mRNA', 'CDS', 'exon', perhaps others?
Thanks,
P. Terry
[email protected]
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