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 <mflawren@fhcrc.org>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 <tanasa@gmail.com> 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]]
>>
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>>
>
>

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