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Old 04-27-2018, 12:54 AM   #1
Alasdeceniza
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Location: Paris

Join Date: Apr 2018
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Default Extract intergenic regions from gff file and keep the strand of neighbour genes

Hello community,
I am working with a gff file and I need to extract all the intergenic regions from there. That is easy, the problem is that I need to classify them (according to the strand of the neighbour genes) in Intergenic-nonSSR (no Strand Switch Regions) if the strand of at both sides of the region is the same, dSSR (divergent SSR) if the strand of the right is + and at the left is -, and cSSR (convergent SSR) if the strand of the right is - and at the left is +. I cannot figure out how to do that and I would appreciate any help on this. Any idea?
Thanks a lot in advance
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