Single cell RNA-seq analysis

Question

[re_raz]

Hi guys I am new to biological field and single cell RNA seq analysis , and I do not have idea how to start I am going to analysis single cell RNA seq which in fastq format to do clustering and get gene expression level, I downloaded the data SRR11804719 What should be the steps to get expression level of all genes in the data? What R package I have to use for analysis? Seurat or 10x single cell RNA-seq analysis?

Answer 1

[jared.andrews07]

There are many options. Seurat is one. The 10X tools are made for 10X protocols, so they are likely not what you want. We cannot run your analysis for you. I'd recommend doing some reading as to how others deal with data using the Seq-Well protocol.

In addition, the Bioconductor Orchestrating Single Cell Analysis book is an excellent in-depth primer on the ins and outs of single cell analysis, whether you use any of their packages or not. I'd recommend reading it, particularly since you admit that you don't even know where to start. That's a pretty solid place.

[re_raz]

Thank you for your replay. As I am new I don not want to lost in huge information on the internet. Could you recommend me good papers about single cell RNA analysis to read?

[ATpoint]

Yes, the linked OSCA workflow. scRNA-seq is a difficult analysis with a lot of things you have to know and many pitfalls. Please do not have the illusion that you can ‚simply and quickly‘ go through a prescripted analysis especially if you are new to bioinformatics, it will take time and a lot of reading and trying-out until you have a solid analysis result that you can stand-up for and confidently present. I recommend not no start with single-cell data and try something else like bulk RNA-seq first for practice since this is easier to digest. Also the size of single-cell datasets simply requires longer runtimes and more memory for most analysis strategies so it simply takes longer to repeat things of something goes wrong. Try some bulk RNA-seq first to get a feel and to get a background in bioinformatics. There are many online resources please google for it.

Answer 2

[ajay nair]

I had found the following tutorials useful when I was picking up the scRNA-seq analysis few years back.

Sanger Instittute

Broad Institute