[BioC] how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer

[Steve Lianoglou]

Hi Yue,

On Thu, May 31, 2012 at 7:23 PM, Yue Li <gorillayue at gmail.com> wrote:
> Not sure if you were asking a question or implying that it's not feasible with UCSC browser. Anyhow, I could just upload to UCSC the bed/bam/bedGraph/gff file containing ranges for multiple chromosomes. Then go to the browser-view to visualize any chromosome in a single window with my browser?

I was just trying to get some clarification is all -- it sounded like
you wanted to see all of the different regions at once when you said:

"""I wonder how to load RangedData for all chromosomes in a SINGLE tab
in UCSC browser using browserView from rtracklayer."""

-steve

>
>
> On 2012-05-31, at 2:12 PM, Steve Lianoglou wrote:
>
>> Hi,
>>
>> On Thu, May 31, 2012 at 1:00 PM, Yue Li <gorillayue at gmail.com> wrote:
>>> Dear List,
>>>
>>> I wonder how to load RangedData for all chromosomes in a SINGLE tab in UCSC browser using browserView from rtracklayer.
>>>
>>> Currently, if I have a GRanges object for "mm9" build:
>>>
>>>> alignGR
>>> GRanges with 238161 ranges and 0 elementMetadata cols:
>>>                    seqnames                 ranges strand
>>>                       <Rle>              <IRanges>  <Rle>
>>>  SRR039212.1000031    chr19 [  8790316,   8790351]      -
>>>  SRR039212.1000085     chr5 [106579844, 106579879]      +
>>>  SRR039212.1000087     chr8 [109778747, 109778782]      +
>>>  SRR039212.1000088     chr8 [ 93777537,  93777572]      +
>>>  SRR039212.1000132     chr3 [128910749, 128910784]      +
>>>  SRR039212.1000149     chr8 [127433402, 127433437]      +
>>>  SRR039212.1000170    chr15 [ 93546853,  93546888]      +
>>>  SRR039212.1000174    chr18 [ 32056273,  32056308]      -
>>>  SRR039212.1000177     chr7 [ 90292453,  90292474]      -
>>>                ...      ...                    ...    ...
>>>   SRR039212.999792     chr2 [162907151, 162907186]      -
>>>   SRR039212.999805     chr6 [ 44021338,  44021373]      +
>>>   SRR039212.999810     chr4 [121106682, 121106717]      -
>>>   SRR039212.999844    chr19 [ 60848841,  60848876]      +
>>>   SRR039212.999848     chr5 [117644397, 117644432]      -
>>>   SRR039212.999854     chr6 [132445007, 132445042]      -
>>>   SRR039212.999855     chr7 [108392362, 108392397]      -
>>>   SRR039212.999892     chr9 [ 20946884,  20946919]      +
>>>   SRR039212.999901     chr2 [168845152, 168845187]      +
>>>  ---
>>>  seqlengths:
>>>        chr1     chr10     chr11     chr12     chr13     chr14 ...      chr8      chr9      chrM      chrX      chrY
>>>   197195432 129993255 121843856 121257530 120284312 125194864 ... 131738871 124076172     16299 166650296  15902555
>>>
>>>
>>> and I do this:
>>>        session <- browserSession()
>>>
>>>
>>>        track(session, "read alignments") <- RangedData(alignGR)
>>>
>>>
>>>        # launch browser view
>>>        browserView(session, alignGR)
>>>
>>>
>>>
>>> This will open 22 tabs in my browser corresponding to 22 chromosomes in the GRanges object. I wonder if it would be possible to have just one single tab open for all 22 chromosomes to view on UCSC browser.
>>
>> Is there anyway that you know of to have the genome browser do what
>> you are asking "directly"?
>>
>> I mean, if you were just navigating w/ the browser alone (not using
>> rtracklayer), how would you get it to do what you are asking?
>>
>> --
>> 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
>



-- 
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