How to make a customized gtf file for differential expression purposes

Question

[Apex92]

Hi everyone.

I need to perform one analysis but not clear how should I start and go through it step by step. It would be great if you share some hints with me.

My purpose is to do differential gene expression analysis but by making my own annotation file. So basically I have my mouse genome GRCm38.p6.genome.fa and want to do Bowtie 1 mapping. But instead of using Gencode annotations, I want to make my own annotations.

I want to bin the mouse genome into ~2.5 million regions that are each 1000 nts long. Then to use FeatureCounts for quantification (dividing weights for multi-mappers) and DESeq2 for identifying differentially expressed regions.

Any help will be appreciated.