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
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