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
