Thread: Tophat problem
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Old 07-15-2009, 03:05 PM   #1
iloveneworleans
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Location: new orleans

Join Date: Jun 2009
Posts: 12
Default Tophat problem

I am trying to supply TopHat with a GFF3 file of gene annotation, the pipeline will report the relative expression of each in the sample.

But I don't know why the <GFF3_file>.expr file is empty and the gff_juncs.log file reports the error message as the following
===========================================
Error: bad transcript annotation:
chr1 hg19_refFlat mRNA 24292939 24306821 . - . ID=FUSIP1;PARENT=FUSIP1;
Offending exons overlapped:
===========================================

Does anyone know the problem or meet the problem before?
Thanks a lot!
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