Yay, it works! Thanks. Bill
On 06/25/2012 03:42 PM, Brian Raney wrote: > 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
