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Old 07-20-2016, 11:57 PM   #42
Simon Anders
Senior Member
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

@SQ SN:gene3013 LN:621
So, each contig/chromosome in your SAM file is a gene. This looks like you aligned to a transcriptome but then tried to proceed with a work flow meant for SAM files aligned to a genome.

I think you got confused about what a GFF3 file is.

Better explain a bit more what you are trying to do.
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