# Analysis of two identical biological paired-end bulk-RNA samples to derive highly expressed TFs

**URL:** https://help.galaxyproject.org/t/analysis-of-two-identical-biological-paired-end-bulk-rna-samples-to-derive-highly-expressed-tfs/15948
**Category:** usegalaxy.eu support
**Tags:** gtn-tutorial
**Created:** [July 10, 2025, 10:35am UTC](https://help.galaxyproject.org/t/analysis-of-two-identical-biological-paired-end-bulk-rna-samples-to-derive-highly-expressed-tfs/15948 "2025-07-10T10:35:39Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![Bilal\_N](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bilal_n/32/7453_2.png) [@Bilal\_N](https://help.galaxyproject.org/u/Bilal_N)
#### Post date: [July 10, 2025, 10:35am UTC](https://help.galaxyproject.org/t/analysis-of-two-identical-biological-paired-end-bulk-rna-samples-to-derive-highly-expressed-tfs/15948/1 "2025-07-10T10:35:39Z")

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Hi, I have two bulk-mRNA samples that are same biologically (basically two replicates). I need to derive a list of highly expressed Transcription Factors in it (no differential gene expression). The sequencing is paired-end.  
Can someone please elaborate how I should go about it ?

Thanks  
Bilal

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### 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 10, 2025, 7:52pm UTC](https://help.galaxyproject.org/t/analysis-of-two-identical-biological-paired-end-bulk-rna-samples-to-derive-highly-expressed-tfs/15948/2 "2025-07-10T19:52:07Z")

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Welcome @Bilal_N

You could follow the steps in one of these tutorial up to the steps right before the DE analysis.

- [Transcriptomics / Tutorial List](https://training.galaxyproject.org/training-material/topics/transcriptomics/)

The End-to-End seems like a good candidate, if your species is one of those supported by the Bioconductor tool **AnnotateMyIDs**. Which species and reference genome do you plan to use?

But I think any of those might work, including this one.

- [Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html)

Hope this helps! 🙂