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
