I am trying to find a way to convert GTF, GCF or even fna assembled genomes to columns, including Fclog2, pvalue, Entrez ID, etc. This is the format one needs for differential gene expression using limma-voom. I’m using bacterial genomes. The tutorial “counts to genes” is optimized for mouse and will not work for bacteria.
Ok, now I understand what you are doing!
As I said before, I think you can use featureCounts for the counting step, even with bacterial genomes.
The other usual option is HTseq-count. Note this will require your annotation to be in GTF format (convert GFF3 to GTF first with gffread as needed).
That other tool is what is used in this much older Galaxy tutorial. Maybe it will be helpful when adapting your methods → RNA-seq - bacteria - Galaxy Australia Training
And, this guide explains the required inputs for the differential expression tutorials and tools. The content on here about making sure your files all fit together is valid for most protocols. → FAQ: Extended Help for Differential Expression Analysis Tools
Hope this helps! 