Question: Doublet in scRNA-seq
0
gravatar for roberts
26 days ago by
roberts30
roberts30 wrote:

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!

seurat rna-seq R • 138 views
ADD COMMENTlink written 26 days ago by roberts30
1
gravatar for ATpoint
26 days ago by
ATpoint41k
Germany
ATpoint41k wrote:

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.

ADD COMMENTlink written 26 days ago by ATpoint41k
2

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.

ADD REPLYlink written 26 days ago by roberts30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1261 users visited in the last hour