[Genome] Finding alternative terminal exons .......

[Rileen]

Hi,
      Thanks once again for the great resource you provide :-)

I've played around with the "knownAlt" track a bit, and was wondering
whether there's any simple way of deriving a list of alternative terminal
exons (ATEs) from it, or any other table/track. By this I mean instances
where the gene has transcripts ending in different exons, not merely
different positions in the same exon.

For all the other events in the knownAlt track, the two positions seem
to provide useful information, but for the altFinish category, they always
seem to differ by 1.

Why is this so?

I was hoping that given the two positions, one cold check whether they
were in two
different exons to derive the list of ATEs as a subset of altFinish,
but that seems
wrong.

Looking forward to your reply,
                                              Yours,
                                                             Rileen

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Rileen Sinha                 rileen at yahoo.com
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