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Bogdan ▴ 660
@bogdan-2367
Last seen 1 day ago
Palo Alto, CA, USA

Dear Aaron, and all, happy and healthy new year !

I was following the tutorial presented at :

https://master.bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/work-3-tenx.html

may I ask, what function do you use in order to remove from a SCE object the barcodes with low total UMI counts

(i.e the empty droplets) ? thanks a lot !

-- bogdan

dropseq dropletutils droplet • 620 views
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... just found the function in the tutorial together with the explanations of the Monte Carlo procedure and the choice of FDR < 0.01 (sorry, 've overlooked it ..)

sce <- sce[,which(e.out\$FDR <= 0.01)]
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Aaron Lun ★ 28k
@alun
Last seen 3 hours ago
The city by the bay

Looks like you solved your own problem. Note that 1% is just a threshold I've used; if you don't like that level of error, you can (and should) set it lower. For example, the BioC-devel versions of the workflows use 0.1%.

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Thank you Aaron. If I may add a question about scRNA-seq analysis (of 10X_Genomics datasets) :

we have 3 experimental conditions to compare (i.e. 3 scRNA-seq datasets : control, treatment1, treatment2).

when I analyze each dataset, i could apply the pipelines that you comprehensively described at :

https://master.bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/work-3-tenx.html

however, shall i compare the specific cell subpopulations in CONTROL vs TREATMENT1 (or TREATMENT2),

which workflow shall I follow (in order to be able to find differentially expressed genes in specific cells) ?

thanks a lot, happy weekend !

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Follow the instructions in the batch workflow to merge all data sets together; cluster cells into subpopulations; and then perform differential expression between conditions within each cluster. This will allow you to identify, e.g., cell-type-specific changes in expression for each cluster. You can also test for differential abundance within each cluster to identify changes in population composition between conditions, a la mass cytometry. I will write up a more detailed workflow on how to do this next month.

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Dear Aaron, thank you very much.

Having a workflow that will give a more detailed example on how to perform differential expression :

1) between conditions within each cluster, and 2) between conditions of different clusters,

would be very very helpful. For our scRNA data analysis, we would like to use at least 2 workflows  :

-- an workflow based on SingleCellExperiment packages that you've written, including "scatter", and "scran"

-- an workflow based on Seurat, at outlined here : https://satijalab.org/seurat/immune_alignment.html