## User: Friederike

Friederike10
Reputation:
10
Status:
New User
Location:
NUC, Weill Cornell Medicine
Last seen:
1 month, 3 weeks ago
Joined:
1 year, 5 months ago
Email:
f******@med.cornell.edu

#### Posts by Friederike

<prev • 6 results • page 1 of 1 • next >
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... sorry, just saw this now. alright, so let's see if I get this right: I should try to find cells that have inconspicuous counts, but low gene numbers. In the example posted today, I excluded cells with less than 500 genes, so I thought I was on the somewhat safe side. Let me check what's going on in ...
written 17 months ago by Friederike10
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... alright. here's the problem: the extreme values do not stem from contaminations. they are, indeed, the marker gene(s) of these particular cells. ...
written 17 months ago by Friederike10
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... thanks, will look into that! PS: I was loosely following your workflow - there you specifically just check for the lower tail when excluding cells based on library size and gene counts, so I didn't pay enough attention to the other end of the spectrum, I guess ...
written 17 months ago by Friederike10
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... Ok, so here's what happened with more stringent filtering of cells (at least 500 genes per cell) - I'll post the code to make sure that it's not just all due to me setting a wrong parameter. # 1. filtering cells > mito.drop <- sceset$pct_counts_feature_controls_mito >= 50 | is.na(sceset$p ...
written 17 months ago by Friederike10
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... Hi Aaron, thanks for the quick reply! * What would you consider "low read count"? With a different data set I tend to follow Seurat's default of min. 500 genes per cell, but this particular data set we wanted to explore rare cell types which is why I've been trying to keep the filtering to a minim ...
written 17 months ago by Friederike10
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... Hi, I've been playing around with different normalization strategies for scRNA-seq data. Contrary to the header, I think, I have actually two questions, the first one being: Is the computeSumFactors() philosophy really applicable to current Drop-seq data sets? The sample that initiated the questio ...
written 17 months ago by Friederike10 • updated 17 months ago by Aaron Lun21k

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