Doublet in scRNA-seq
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11 months ago
roberts ▴ 40

Hello, I did 10X scRNA-seq I want to filter out any doublets since we had a high number of cells read. Does anyone have any suggestions?I tried DoubletDecon but I am not familiar with shiny so could not figure out how to use it. Thanks!

RNA-Seq R Seurat • 1.1k views
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11 months ago
ATpoint 54k

Look, and I know this is probably not what you want to hear, but why don't you spend a couple of days reading online resources and trying things out. This is better than opening a question for every upcoming problem. It takes time to get into a new method such as scRNA-seq analysis, but it is recommended that you first get familiar yourself a bit. There is also https://osca.bioconductor.org/ which extensively described single-cell workflows using the Bioconductor environment. For me this is way better documented than Seurat, and therefore easier to digest, better to get my head around. I strongly recommend it over Seurat, maybe give it a try, it contains lots of useful information and material plus example code. I personally found http://www.bioconductor.org/packages/release/bioc/html/scDblFinder.html helpful in my analysis.

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I know it may not seem like it but I actually do spend a long time trying to find an answer before I post a question. I am new to bioinformatics and computer science as a whole. I get very lost very quickly, and I don't have access to anybody to answer my questions-- hence my use of this public forum. I understand that my questions may seem trivial to you but to me they are problems I really need help figuring out. That being said thank you for the resources and help.

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