Hi Aaron, Thank you for sending more detail. This is being added to the development queue for prioritization.
We appreciate your input! Jen UCSC Genome Browser Support On 7/10/10 10:55 PM, Aaron Wenger wrote: > Hiram et al - By that I mean a BED track that obtains data from multiple > tables, with the option to turn certain tables on or off from the track > configuration page. For example, all of the "peak" subtracks from the > Yale TFBS supertrack would be displayed as if they were all loaded as a > single track, without each subtrack always claiming a line of space. > The Yale TFBS is probably the best example to me. It has ChIP-seq data > for tens of factors, most of which do not have binding sites at a given > locus. Yet, if I want to see all the different TFs, the subtracks > always claim tens of lines of vertical space. I'd like to display the > data as if it were a single track drawn from the separate database > tables. Jim Kent presented essentially that idea on slide 18 of his > presentation at > http://users.soe.ucsc.edu/~kent/presentations/encodeDc2010.pdf. > > I appreciate the help. > > Aaron > > On 7/10/2010 4:34 PM, Hiram Clawson wrote: >> What would a multi bed type of track look like ? >> >> ----- Original Message ----- >> From: "Aaron Wenger"<[email protected]> >> To: [email protected] >> Sent: Saturday, July 10, 2010 3:09:33 PM GMT -08:00 US/Canada Pacific >> Subject: Re: [Genome] [Genome-mirror] "Combined" composite tracks >> >> Pauline - Thank you for the reply. >> >> It's good to see the feature available for wiggle tracks, but I'm >> primarily interested in a "multiBed" type track. Does that exist? If >> not, are there plans to develop it? >> >> Thank you, >> Aaron >> >> On 7/9/2010 5:54 PM, Pauline Fujita wrote: >> >>> Hello Aaron, >>> >>> This is still a feature in development but is almost ready for >>> release. In fact the first tracks to use this feature will be under >>> quality assurance review shortly. >>> >>> For the first releases this won't be something you can do with a >>> custom track but will be possible if you are running a mirror. Here is >>> a sample of the trackDb.ra entries that are needed for these first >>> releases: >>> >>> track wgEncodeRegTxn >>> container multiWig >>> noInherit on >>> type wig 0.00 2716.04 >>> superTrack wgEncodeReg hide >>> shortLabel Transcription >>> longLabel Transcription levels assayed by RNA-seq from ENCODE >>> release alpha >>> configurable on >>> visibility full >>> maxHeightPixels 100:30:11 >>> showSubtrackColorOnUi on >>> aggregate transparentOverlay >>> transformFunc LOG >>> viewLimits 0:4 >>> priority 1 >>> >>> track wgEncodeRegTxnGm12878 >>> table >>> wgEncodeCaltechRnaSeqRawSignalRep1Gm12878CellLongpolyaBb12x75 >>> shortLabel Gm12878 >>> longLabel Transcription of Gm12878 cells from ENCODE >>> release alpha >>> parent wgEncodeRegTxn >>> type wig 0.00 2446.53 >>> color 255,128,128 >>> >>> track wgEncodeRegTxnH1hesc >>> table wgEncodeCaltechRnaSeqRawSignalRep1H1hescCellPapBb2R2x75 >>> shortLabel H1 ES >>> longLabel Transcription of H1 ES cells from ENCODE >>> release alpha >>> parent wgEncodeRegTxn >>> type wig 0.00 3686.36 >>> color 255,212,128 >>> >>> Note that the key new tags here are "container multiWig" and >>> "aggregate transparentOverlay" in the parent track. You don't need to >>> do anything different on the wigs that make up the subtrack. The >>> "table" tag is new. It lets you use the same table in multiple tracks >>> among other things. I think if you've got the latest released binary >>> CGIs they'll silently support this already. >>> >>> Hopefully this information was helpful and answers your question. If >>> you have further questions or require clarification feel free to >>> contact the mailing list at [email protected]. >>> >>> Regards, >>> >>> Pauline Fujita >>> UCSC Genome Bioinformatics Group >>> http://genome.ucsc.edu >>> >>> >>> >>> >>> >>> On 07/02/10 14:54, Aaron Wenger wrote: >>> >>>> Hello, >>>> >>>> Does the "combined" subtrack feature that is featured on slide 18 of >>>> Jim Kent's presentation at >>>> http://users.soe.ucsc.edu/~kent/presentations/encodeDc2010.pdf online >>>> yet, or is it still future work? I have a number of subtracks that >>>> are sparse, which means that I have a lot of empty lines just eating >>>> up vertical space. The combined feature is exactly what I need. If >>>> it's not available, do you have any suggestions on other ways for me >>>> to achieve that effect? Is there somewhere I could add a custom >>>> track handler? >>>> >>>> Thank you, >>>> Aaron >>>> _______________________________________________ >>>> Genome-mirror mailing list >>>> [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror >>>> >>> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
