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Old 07-19-2011, 09:49 AM   #1
sdarko
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Location: Bethesda, MD

Join Date: Apr 2009
Posts: 51
Default TopHat Warning: Encountered reference sequence with only gaps

Hi,

I received the following warning during a tophat run earlier today.
Code:
[Tue Jul 19 11:55:37 2011] Indexing splices
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Can anyone explain to me what that might mean?

Thanks,
Sam
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Old 04-19-2012, 01:26 PM   #2
ataheri
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Location: Nashville, TN

Join Date: Nov 2011
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Did you find the answer to your question? I am facing the same problem with my Data as well.
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