I just finished running some single nucleus rna seq fastq files through Cellranger's count pipeline and I received this warning:
Low Fraction Reads in Cells 67.0% 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.
There are 6 samples and all of them have low fraction reads (~54%-67%). Here is the call format:
cellranger count --id=A1 --fastqs=data/sample_data/fastqs/A1_S1_L001 --sample=A1 --transcriptome=data/reference_data/cellranger_ref_data/mouse_mm10-3.0.0 --include-introns --localmem=128 --localcores=32
This is my first time working with snRNA-seq data and it is not clear to me if this is typical for single nucleus data or if there was something that happened during library prep/isolation/sequencing processes. Any guidance or suggestions/thoughts are _greatly_ appreciated, thank you in advance.