Michael, thank you very much again. On the same topic, if these 2 experiments have a different number of total tags,
let's say 10 mil and 3 mils, and I would like to plot the tag densities in the promoter regions for each experiment, what is a good way to normalize the data and make the tag density plots comparable ? thanks again - with much appreciation, bogdan On Wed, Aug 26, 2009 at 5:45 AM, Michael Lawrence <[email protected]>wrote: > The GenomicFeatures package has transcript information from the UCSC > database. > > library(GenomicFeatures) > data(geneHuman) > > ## filter for reads in hg18 chr1 promoter regions (by default, -500,500 of > TSS) > > trans <- transcripts(geneHuman) > promoters <- Views(cov, trans["chr1"]$promoter) > viewSums(promoters) > > ## trans also includes whole transcript, upstream, downstream and > threeprime regions > ## you can do the same for introns, exons > introns <- Views(cov, ranges(introns(geneHuman))[[1]]) > exons <- Views(cov, ranges(exons(geneHuman))[[1]]) > > Michael > > On Tue, Aug 25, 2009 at 10:41 PM, Bogdan Tanasa <[email protected]> wrote: > >> Hi everyone, >> >> to add another question - I would highly appreciate if you could let me >> know >> >> any quick way to obtain the ChIP-seq tag density plots in the vicinity of >> various >> genomic elements - eg promoters, introns, or given a custom list ? thanks >> again. >> >> -- bogdan >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
