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
--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!
1 answer
The web summary information would be almost exactly the same as what you already have. Unless you are absolutely sure what you are doing, I'd let 10X decide the barcode cut-off. Being a percent and a half under the QC cutoff isn't much of a reason to second guess them.
Log in to answer this question.
-
Low Fraction Reads in Cells (Cellranger Count Pipeline)
written by Cricket •
-
FASTQC after trimming: how do I know if it is good enough to proceed to alignment?
written by whb •
-
vlm.adjust_totS_totU -- Input contains NaN, infinity or a value too large for dtype('float64')
written by ericrkofman •
-
Result of scanpy tools rank_genes_groups
written by el24 •
-
Unbalanced design and large difference in number of input reads for DESeq2
written by JW •
-
featureCounts: Low % assigned fragments and discrepancy between STAR alignment multi mapped reads
written by david.gonzalez •
-
GSVA R packages
written by Morris_Chair
-
BiomaRt Many to Many Relationship filtering
written by iislam •
-
sva combat removes wanted biological variation
written by exin
-
why polyQ are not part of intrisicaly disordered region (IDR) in disopred3 prediction?
written by boaty
I just checked a reanalyze of mine, and it's the same. Nothing on the front tab. New t-SNE on the second tab.
Thanks for checking, do you have any idea how can I safely remove the cells with fewer read values (which are not reliable) so that I can get the barcode rank plot and summary information in my web_summary.html? Also, do you usually recommend using any other parameters in "cellranger reanalyze" or you think my script is fine?
I appreciate it if you have any recommendations! Thanks!