gravatar for el24

2 hours ago by


Hi everyone,

I have a question regarding running cellranger count on the data, I get the following warning after running it:

Low Fraction Reads in Cells

68.5%   Ideal > 70%. 

Application performance may be affected. Many of the reads were not assigned to cell-associated barcodes. This could be caused by high levels of ambient RNA or by a significant population of cells with a low RNA content, which the algorithm did not call as cells. The latter case can be addressed by inspecting the data to determine the appropriate cell count and using --force-cells.

Then, as suggested I run cellranger reanalyze using the following command to get 900 cells:

cellranger reanalyze --id=reanalysis_900 
--matrix=/PATH/outs/raw_feature_bc_matrix.h5    #cellranger count output

When I check web_summry.html it doesn't include the summary of the data or any plots in the "summary tab", it's just a blank page with trivial information. I have tried another number of for the force cells (600), but it didn't help. (I originally got about 1200 cells when running cellarnger count in the web_symmary.html output)

Could anyone give me a clue if I'm doing anything wrong? Do you have any recommendations to get the barcode rank plot and summary information in my web_summary.html?


I appreciate it!
Thanks a lot!


modified 53 minutes ago



2 hours ago


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