[Genome] xenoRNA download from Orangutan database

[Brooke Rhead]

Hi Jason,

The xenoRNA track is in PSL format, described here:

http://genome.ucsc.edu/FAQ/FAQformat#format2

Within the description on this page is this crucial bit of information:

~~~
Be aware that the coordinates for a negative strand in a PSL line are 
handled in a special way. In the qStart and qEnd fields, the coordinates 
indicate the position where the query matches from the point of view of 
the forward strand, even when the match is on the reverse strand. 
However, in the qStarts list, the coordinates are reversed.
~~~

Please feel free to write back to genome at soe.ucsc.edu if you have 
further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Blythe, Jason wrote:
> Hello-
> 
> I have a question about a few fields that are seen in the Orangutan
xenoRNA track download from the browser. The fields in question are
tStart,tEnd,and tStarts. I have only checked this for a few of our
results, but if one lies on the negative strand ('+-') the tStarts
listed do not fall within the parameters of tStart and tEnd(Ex. BC042829
chr7:84009419-84017370). However the ones listed on the positive stand
('++') are all good. Is there something that I am missing if there is an
RNA that is on the negative strand that I should be accounting for? Thanks.
> 
>  
> 
> jason 
> 
> 
> 
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