merging single cell and bulk sequencing data

Question

[Meghan.T]

I'm pretty new to working with NGS data . I want to do a classification on sequencing profiles from different body organs. for some tissues I have both single cell and bulk sequencing data and for the rest I only have bulk sequencing data. My question is how to merge single cell and bulk sequencing data? and is this kind of merging usually advised or discouraged?

[Friederike]

As always the answer is "it depends". As you are new to the field, I would advise against it as the pitfalls are plenty and probably subtle at times. I would hope that there's bulk RNA-seq data out there for almost every single type of cell except the very rare ones, so my first response would be to send you back to GEO or wherever you looked for RNA-seq data and dig up the bulk RNA-seq data for the samples you currently only have single-cell RNA-seq data for.

[ATpoint]

Can you elaborate on what exactly you want to do? "Classify" is such a broad term. I doubt that you can merge (in terms of really combine) datasets. scRNA and bulk are too different. Maybe some smart classifications strategy, e.g. SingleR just to name one, could help here. Please add details.