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Old 03-03-2011, 10:17 AM   #1
poisson200
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Location: united kingdom

Join Date: Feb 2010
Posts: 63
Default Tophat; warning

I have ran Tophat on 50bp paired-end Illumina data and it generates quite a few warnings as below.

[Thu Mar 3 09:35:27 2011] Indexing splices
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
many more lines of this.

Is this something to be concerned about? I am using HG19 which was indexed using the latest Bowtie-build;

bowtie-build version 0.12.7
TopHat v1.2.0

Thanks for any tips.

John.
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