I am running the analysis for non-model strain for which reference sequence is in scaffolds and annotation is still in progress. I obtained a set of variants of interest and I annotated them with snpEff and later on find possible functional context of variants in coding sequences running Blast2GO search. However, most of variants (over 98%) falls into intergenic regions - annotation for those looks as follows:
Is there any way to get more information about variants in intergenic regions? For example predict some promoters/regulatory regions? It seems to me like most of the tools are based on annotations available in databases which is not the case for me. Focusing on variants in coding sequences only makes the scope of my analysis very narrow but as I lack experience I don't really know how to proceed further.
Thanks in advance! Agata