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

[Bilal_N]

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

[jennaj]

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

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

Hope this helps!