Closed wangjiawen2013 closed 1 month ago
And this is the way to generate the plot:
This plot shows the Sequencing Saturation metric as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. Sequencing Saturation is a measure of the observed library complexity, and approaches 1.0 (100%) when all converted mRNA transcripts have been sequenced. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point. The dotted line is drawn at a value reasonably approximating the saturation point.
Could we subsample the RAD file outputed by simpleaf ?
Hi @wangjiawen2013,
The necessary values to compute these plots are in the set of output features of alevin-fry
. I'm cc'ing @ygao61 and @csoneson who have created such plots from the alevin-fry
output before and who can instruct you as to the best way to generate such a plot.
--Rob
Hi @wangjiawen2013,
Below are the steps you can follow to generate the sequence saturation plot:
alevin-fry
quant output folder.--Yuan
Got it. Thanks!
Hi, I can get sequencing saturation curve using cellranger from 10x genomics single cell data. How to get it using simpleaf ? This is the definition of sequencing saturation (https://kb.10xgenomics.com/hc/en-us/articles/115003646912-How-is-sequencing-saturation-calculated):
And this is an example plot: