Thanks for the information. It had been very helpful.
Best regards,
Khadeeja




On Sunday, October 27, 2013 7:05 AM, Michael Lawrence <lawrence.michael@gene.com> wrote:
 
If it's in UCSC, you can probably find the right track in AnnotationHub. 

Michael




On Sat, Oct 26, 2013 at 5:02 PM, khadeeja ismail <hajjja@yahoo.com> wrote:

Hi Michael,
>
>
>We obtained a list of about 80 probes from differential methylation analysis, mapping to genes associated with the phenotype we are studying. One of my colleagues had been looking at the probes one by one on genome browser, to see if the CpG site was anywhere near a regulatory region, but the task turns out too tedious. So we wondered if we can get the locations for the regulatory regions and find overlaps with the CpG sites. There are probably better ways to do it. I had a look at ggbio and GViz on BC website, and I'm definitely going to try them asap. Meanwhile I hope I have made my problem a bit more clearer, and if you have any other suggestions I'd be more than happy to know. Thanks a lot! I might be coming back with more questions soon.
>
>
>
>Regards,
>Khadeeja
>
>
>
>
>On Sunday, October 27, 2013 12:20 AM, Michael Lawrence <lawrence.michael@gene.com> wrote:
> 
>Please give a little more detail about your problem. If the number of
>probes is large enough, you might want to summarize the overlaps and plot
>the summaries, rather than looking at every region individually. If you did
>want to go that route, it would be best to use ggbio and/or GViz to
>automate the plotting. The UCSC browser is simply not designed for batch
>plotting.
>
>Michael
>
>
>
>On Thu, Oct 24, 2013 at 9:37 AM, khadeeja ismail <hajjja@yahoo.com> wrote:
>
>>
>>
>> Hi,
>> I am working  with some 450k array probes which I need to look up in
>> Geneome browser to see in which type of areas these probes are located in.
>> For example, if the CpG site (+/- 100kb) overlaps with any of the following
>> in the GM12878 track.
>>
>>
>> Layered H3K27Ac
>> Layered H3K4Me1
>> Layered H3K4Me3
>> Transcription
>> DNase Clusters
>> DNase Clusters V1
>> Txn Fac ChIP V3
>> Txn Factor ChIP
>>
>>
>> I would like to do it as batch and not one by one since the list of probes
>> is long. I have tried querying the GenomeBrowser database and also the
>>
 rtracklayer package in R but have not been successful. Would be great if
>> anyone can give me any ideas on how it can be done.
>>
>> Thanking you,
>> Khadeeja
>>         [[alternative HTML version deleted]]
>>
>>
>
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>>
>
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