ME034V_Gene_TE_Expression.md

Do TEs in introns (or heavily methylated introns) impact expression of pre/post TE-intron exons?

First we need to identify 2 distinct sets of genes

1. Those B73 genes with at least 3 introns AND zero bp annotated as TE that ARE expressed
2. Those B73 genes with at least 3 intrins AND a structural TE >= 1kb (or a mCHG criteria?)that ARE expressed

This represents the extreme edges of TE-genes (or methylated genes) - if we see differences here we can dig in, if not, we are unlikely to see differences in genes in other places on the spectrum

Creating the gene sets