Great tool :) I'm just wondering about the gene promoter annotation.
In CRE.info.tsv the gene_promoter value is either annotated, unannotated or none. I understand that gene_promoter = annotated applies to CREs that are both proximal and on the same strand (ss) as a matching transcript TSS. And all CREs where gene_promoter = unannotated are on the same strand (ss) and have regionType listed as either "exon" or "intron".
But I also have many thousands of CREs with ss and regionType = exon | intron that are simply listed as gene promoter = "none".
So is there an extra piece of information deciding whether to call a CRE as an unannotated promoter? And if so what is that?
Great tool :) I'm just wondering about the gene promoter annotation.
In CRE.info.tsv the gene_promoter value is either annotated, unannotated or none. I understand that gene_promoter = annotated applies to CREs that are both proximal and on the same strand (ss) as a matching transcript TSS. And all CREs where gene_promoter = unannotated are on the same strand (ss) and have regionType listed as either "exon" or "intron".
But I also have many thousands of CREs with ss and regionType = exon | intron that are simply listed as gene promoter = "none".
So is there an extra piece of information deciding whether to call a CRE as an unannotated promoter? And if so what is that?