quantification for unannotated loci

Question

[jia]

Hi, everyone！I have eight RNA-seq data (two condition,replicate =4), and found a unannotated loci with upregulated transcription from the merged bw file.

Now I want to quantificate the transcription of this loci from these 8 RNA-seq data and then calculate the correlation between this loci and the nearest gene, just like the following picture. Thanks advance! ![unannotated loci]

[ATpoint]

So what is the exact question please? Do you need software, or code? Some context would help.

[jia]

Thank you for your timely reply! Yes, I need some code to fix this problem, please share it with me if that possible? Or is there any software that I can use?

[ATpoint]

Ok, but please add details. So what are you actually quantifying with right now? A GTF file, peak files? What exactly do you need? Like adding new regions to the reference?

[jia]

I have bam files, bw files and the hg38 GTF file, but no peak file. I saw increased transcription at a loci from bw files (no coordinate). I want to quantify the transcription of this unannotated loci. So first I don't have coordinates of this loci, can I manually select a region for quantification? Or maybe I can obtain the coordinates from the bam files? and if i have the coordinates , how can I add this regions to the GTF file? It seems that the GTF files contains for each gene a hierarchy of information as: gene, transcript, exon.