Hey Bill, If you add the following four lines to each of your BAM stanzas in your track hub, it should make the display of your BAM tracks the same as they are displayed in custom tracks:
baseColorDefault diffBases baseColorUseSequence lfExtra bamColorMode strand showDiffBasesAllScales . Brian Raney On Mon, Jun 25, 2012 at 2:50 PM, William Noble <[email protected]> wrote: > > > On 06/25/2012 01:23 PM, Luvina Guruvadoo wrote: >> Hi Bill, >> >> The options you are referring to are explained in some detail on our >> BAM configuration help page, please see: >> http://genome.cse.ucsc.edu/goldenPath/help/hgBamTrackHelp.html. > > Thank you for this pointer. > >> The BAM tag definitions can be found in the SAM tools documentation: >> http://samtools.sourceforge.net/. The BAM coloring modes should allow >> you to get the same results as uploading a custom track. >> > > Alas, I cannot figure out, from the documentation, what is going on > here. Here is a little bit of the display I'm seeing: > > > > The top track was uploaded via the "manage custom tracks" button on the > browser. The second track was uploaded via my track hub. Both tracks > are using the same BAM file. On the top is the representation that is > described in the documentation, with strand encoded as dark red or blue, > and mismatches indicated by bright red vertical bars. However, in the > version uploaded via my track hub (below), strand is doubly represented, > both as color and using a series of "<" or ">" symbols. I can find no > way to get rid of these ">" symbols, no mention of them in the > documentation, and no way to turn on the default mode of indicating > mismatches with a bright red bar. > > Can someone help me debug this problem? > > Thanks. > Bill > > >> Please contact us again at [email protected] if you have any further >> questions. >> >> --- >> Luvina Guruvadoo >> UCSC Genome Bioinformatics Group >> >> >> On 6/21/2012 9:38 AM, William Noble wrote: >>> On 06/20/2012 03:07 PM, Steve Heitner wrote: >>>> The sections you will want to view are: >>>> >>>> http://genome-preview.cse.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html#c >>>> >>>> ommonSettings >>> At the URL above, I found this documentation for the "|bamColorMode" >>> tag: >>> >>> | >>> >>> |bamColorMode<strand/gray/tag/off>| >>> >>> There are numerous ways to color bam tracks to highlight certain >>> aspects if the data. All of these are user configurable. By >>> default, >>> mismatched bases are highlighted in bright red, and alignments to >>> the plus strand are colored dark blue and minus strand are dark >>> red. >>> >>> I am wondering how to interpret the four options (strand, gray, tag, >>> off). Is there a description somewhere of what these options mean? >>> >>> The motivation for this question is that I have a BAM file that I >>> uploaded via a track line in the "Upload custom data tracks" dialog and >>> also put into my track hub. Using the first mode, I see the BAM file in >>> the default coloring (by strand, with mismatches colored in bright >>> red). However, via my track hub, the mismatch coloring disappears and >>> instead I get ">" or"<" signs indicating, I think, pairing >>> information. I want the track hub version to display in the default >>> mode. Can someone let me know whether this is possible, and how to >>> do it? >>> >>> Thanks. >>> Bill >>> >>> >>> _______________________________________________ >>> 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
