Applicability of SPLASH for Prokaryotic Transcriptome Analysis in a Symbiotic System

[XiaoluLLLLLiu]

Dear SPLASH developers,

I am currently working with metatranscriptomic data from a highly specialized symbiotic system consisting of only a single methane-oxidizing bacterium. Since SPLASH is a reference-free method designed to identify sequence variation from raw sequencing reads, I am interested in evaluating its potential for analyzing prokaryotic transcriptomes.

In eukaryotic systems, SPLASH has been demonstrated to detect various RNA-level events such as alternative splicing, RNA editing, gene fusions, and transposable element mobilization. However, prokaryotic transcriptomes are inherently different, as they lack alternative splicing and generally have more compact genome structures.

I would like to ask:

Does SPLASH have potential applications in detecting RNA-level variations in prokaryotic transcriptomes?
For example, could it be useful for identifying RNA editing, transposon activity, or novel regulatory elements in bacteria?
Has SPLASH been tested on bacterial transcriptomic data before?
Would you recommend SPLASH for analyzing metatranscriptomic data from a single-species microbial symbiosis?
Are there any known limitations or adjustments required when applying SPLASH to prokaryotic RNA-seq data?
Since my dataset consists of a single bacterial species in a symbiotic environment, I believe it could serve as a well-controlled case study for testing SPLASH in prokaryotic systems. I would greatly appreciate any insights or recommendations you could provide.

Thank you for your time!

Best regards,
Xiaolu

[roozbehdn]

Hi Xiaolu,

SPLASH cn essentially identify any sort of variation as long as it is statistically varied among inoput samples. We have not tried splash on metatranscriptomic, but it has been used for a microbial analysis. You can have a look at the paper here:
https://www.biorxiv.org/content/10.1101/2024.01.18.576133v1.abstract