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.
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manuelmourato25 •
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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.