On Mon, Oct 25, 2010 at 1:33 PM, Paul Shannon
<pshannon@systemsbiology.org>wrote:

> I've tried hard to come up with a minimal example of this -- some fragment
> of code to reproduce the error -- but I haven't figured out yet how to do
> that.  So instead, and thinking that a brief report might be useful, and
> will possibly trigger something in Michael's mind, I send this narrative
> email instead.
>
> I create a track with this command:
>
>   track (session, 'exonHits') = grange   # a GRangesForUCSCGenome object
>
> Then I ask to look at the track:
>
>   view <- browserView (session, range.to.view, full='exonHits',
> dense='ruler', hide=trackNames (session))
>
> The problem is that sometimes I get this error:
>
>   Error in resolveTrackIndex(x, i) : Unknown track(s): exonHits
>
> When I look for the 'exonHits' track, I learn that there are actually two
> of them, each with a suffix:  "exonHits m" and "exonHits p"
>
>    > grep ('exonHits',  trackNames (session.sub), ignore.case=T, v=T)
>             exonHits m          exonHits p
>     "ct_exonHitsm_7841" "ct_exonHitsp_7844"
>
> I can use these odd, modified track names, and display the desired:
>
>   view <- browserView (session, range.to.view, full='exonHits m',
> dense='ruler', hide=trackNames (session))
>
> But it seems rather suspicious.  Is there any reason for the 'm' and 'p'
> suffixes?
>
>
You've caught another undocumented feature. The graph formats like  "wig" or
"bedGraph" do not encode a strand. Since UCSC supports multiple tracks, if
values come from multiple strands, we split them up, for the (m)inus and
(p)lus strands. If this is not desirable, just set the strand on all
features to "*".


> Thanks,
>
>  - Paul
>
>
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