[BioC] ChIPpeakAnno, building annotations
Hans-Rudolf Hotz
hrh at fmi.ch
Tue Aug 24 17:49:31 CEST 2010
Marc
Use "rtracklayer" which interfaces with the UCSC genome browser. You
have access to all the tables with the "track" function. Have a look at
help for "track". - This corresponds to using the following web page:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
In your case, you need the "RepeatMasker" track. From the data you get
back, you need to select for the different alu types. You do get all
repeats.
For CpG islands, take the "CpG Islands" track
Hans
On 08/24/2010 04:52 PM, Marc Noguera wrote:
> Hi all,
> I have been learning to use ChIPpeakAnno package to annotate the peaks I
> obtain with CHiPseq experimetns. I see that, useing biomaRt, i can get
> to some annotation on ensembl and annotate the peaks according to TSS,
> exon, miRNA and some other features.
> I would like, also, to be able to search for repetitive elements, such
> as ALUs and CpG Islands. Is that kind of information also accessible
> using biomaRt? I can't seem to find it. If not how should I proceed?
>
> Thanks in advance
>
> Marc
>
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