Hello all,
I have some feature matrixes from a bulk RNA seq analysis pipeline, and I want to perform bulk deconvolution to get relative single cell proportions. Some of the samples are from WT mice, while others are from mices with an induced condition.
I have also acquired a single cell dataset for the tissue and cell types ( around 40) that I want to analyze.
I have tried to use Music2 to perform this deconvolution, but the only times it converges are when I specify two or three cell types to get the proportions. When I specify more than that, it usually does not converge or it runs for 20+ hours without returning a result.
My question is, is there any similar tool to Music2 that does not require a single cell reference dataset for the disease induced samples? I can only find ones such as CIBERSORT that only work when both scRNA datasets are available.
Thank you.
It's mice. Why don't you get another set of them, repeat the experiment and do a proper flow cytometry panel. Then you know the proportions without fiddling with these blackbox algorithms.
ATpoint appreciate the feeback regarding this question. Regretfully I am not in a position to repeat the experiments, as I am merely assisting with the development of the bioinformatics and data analysis workflow. Also I have been made aware that single cell sequencing of this caliber has high associated costs to it. I will however keep your comment in mind. Regarding the mice typo, thank you, I did spell it correctly five words before, but had a split of the keyboard there :)
Flow cytometry, FACS, not sequencing.