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Old 10-16-2018, 11:53 AM   #1
Location: US

Join Date: Apr 2010
Posts: 63
Default Remove duplicate genes/mRNA from a gff file

I would like to combine two different gff files and then remove some duplicate genes/mRNA/exons with overlaps. I did not find any tool to do it. There is an option using bedtools to merge two gff files, but not to remove these duplications. Also, I can do it using blast, but there are too many steps, I am looking for something relatively simple.
These overlaps are the ones with different IDs, but same or similar coordinates (with some % of overlap).
Any suggestions?
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annotation file, duplicates, gff, gff3

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