# Genomes in columns for limma-voom.

**URL:** <https://help.galaxyproject.org/t/genomes-in-columns-for-limma-voom/12983>\
**Category:** usegalaxy.org support\
**Tags:** transcriptomics\
**Created:** [July 15, 2024, 7:47pm UTC](https://help.galaxyproject.org/t/genomes-in-columns-for-limma-voom/12983 "2024-07-15T19:47:11Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Daniel\_Sonenshine](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/daniel_sonenshine/32/5402_2.png) [@Daniel\_Sonenshine](https://help.galaxyproject.org/u/Daniel_Sonenshine)\
**Post date:** [July 15, 2024, 7:47pm UTC](https://help.galaxyproject.org/t/genomes-in-columns-for-limma-voom/12983/1 "2024-07-15T19:47:11Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [July 15, 2024, 10:52pm UTC](https://help.galaxyproject.org/t/genomes-in-columns-for-limma-voom/12983/2 "2024-07-15T22:52:54Z")

</div>

Hi @Daniel_Sonenshine

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](https://galaxy-au-training.github.io/tutorials/modules/dge/)

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](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_differential_expression_help.html)

Hope this helps! 🙂