Currently I am working with pool-seq data and I am specifically interested in SNPs and underlying genes with significant differentiation. I was able to find several thousands of SNPs that show significant differentiation after correcting for multiple testing. Now I want to look at the genes underlying these SNPs. Since I am working with pool-seq data I am working with the Popoolation(2) software package. This package contains a script to create a genewise-sync file which enables you to check for genes that are particularly enriched with high differentiation SNPs. This is the point where I am stuck. When trying to create the genewise sync file I get the following error: "all features of a gene have to be on the same strand; Problem for BG8803808". When I check the gene, I see that a CDS and an exon are indeed annotated to the opposite strand from the rest of the features. So here's my question: is it common for an annotated (draft) genome to have features of the same gene on both strands? And how can I solve this issue (maybe write a costum script to find the genes using my set of SNPs)?
Thanks in advance,