[BioC] Get all 3'utr and 5'utr region from GenomicFeatures

[Steve Lianoglou]

Hi,

On Tue, May 24, 2011 at 11:34 AM, Fabrice Tourre <fabrice.ciup at gmail.com> wrote:
> Steve,
>
> It make sense.
>
> Thank you very much.

Nice -- one last thing.

If you will be taking the Views route, read through this recent thread
from the bioc-sig-seq mailing list:

https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011-May/001985.html

In particular this (very detailed) explanation from Herve about
when/how you might want to use compact with Views so that you don't
end up trying to store your entire genome in RAM:

https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011-May/002000.html

Hope that helps,
-steve


>
> On Tue, May 24, 2011 at 5:19 PM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>> Hi,
>>
>> On Tue, May 24, 2011 at 9:18 AM, James W. MacDonald
>> <jmacdon at med.umich.edu> wrote:
>>> Hi Fabrice,
>>>
>>> On 5/24/2011 4:56 AM, Fabrice Tourre wrote:
>>>>
>>>> Dear list,
>>>>
>>>> How can I get all 3'utr and 5'utr region from GenomicFeatures of Human?
>>>> There are fiveUTRsByTranscript, threeUTRsByTranscript methods in
>>>> GenomicFeatures. But how can I get these regions?
>>>
>>> hg19 <- makeFeatureDbFromUCSC(genome = "hg19", table = "refGene")
>>> utr3 <- threeUTRsByTranscript(ref19)
>>>
>>> Which seems pretty obvious to me, given the help pages for these functions.
>>>
>>> It would be helpful if you could give us an indication of where you got
>>> stuck, and what in particular you didn't understand from the help pages, so
>>> we can improve our documentation.
>>
>> Perhaps the OP wanted to know how to get the sequences from those
>> regions, given the results from those functions?
>>
>> If that's the case, I'd load up the BSgenome.Hsapiens.UCSC.hg19
>> library, iterate over my results one chromosome at a time, and use a
>> mix of the Views function over the unmasked chromosome (using ranges
>> across the 3'utr across the chromosome as the second argument) ...
>> you'll have to take care of seqs on the reverse strand.
>>
>> You could also look at the getSeq function.
>>
>> I'lll leave the actual writing of the code as an exercise to the
>> reader since I think it's useful to know how Views work and you'll
>> have to read up on the documentation a bit :-)
>>
>> -steve
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>  | Memorial Sloan-Kettering Cancer Center
>>  | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
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>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact