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07-15-2009, 03:05 PM
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Member
Location: new orleans Join Date: Jun 2009
Posts: 12
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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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