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-   -   Extract intergenic regions from gff file and keep the strand of neighbour genes (http://seqanswers.com/forums/showthread.php?t=82080)

Alasdeceniza 04-27-2018 12:54 AM

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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