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

[Yue Li]

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?


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