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mattanswers 10-04-2016 10:54 AM

gene overlaps in Arabidopsis GFF file
Has anyone ever looked at a GFF to find all the genes that have base overlaps ?
These genes can be counted a 0 in HTSeq and Arabidopsis is a dense genome, so I was wondering if anyone has done this before, or if they have done so with another genome and have some coding tips.

Genes will overlap with themselves, and I want to avoid that, and genes will also overlap with the chromosome they are located on and I want to avoid that as well. Just wondering if there anything out there already with this information, or if there were some computational tools that would be helpful.

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