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. 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.
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
