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 --force-cells=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!