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

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