10X Genomics -- Pipeline Run Details
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Sample ID: 10x_output
Reference: /yoshitake/test/linkage-analysis~single-cell_CellRanger-VarTrix/refdata-pseudochr.re
ALERT: Fraction of reads with valid barcodes is 84.7%. Ideal > 85%. This usually indicates a quality issue with the first 16 bases of read 1. This will result in an incorrect assignment of reads to cells and copy number calls are likely to be affected.
ALERT: Fraction of noisy cells is 54.7%. Ideal < 50%. A large fraction of cells have high variance in the read coverage profile. Copy number estimation in these cells can be severely impacted. Causes include a large fraction of cells undergoing DNA replication or a sample that is highly rearranged relative to the supplied genome or a problem during library preparation.
ALERT: Fraction of reads not in cell barcodes is 41.2%. Ideal < 10%. A large fraction of reads not in cell barcodes could be a consequence of free floating DNA or a problem during library preparation. Copy number estimation for cells is unlikely to be impacted.
ALERT: Length of shortest primary contig is 5943460 bases. Ideal > 10,000,000 bases. Copy number estimation on contigs shorter than 10 megabases can be inaccurate, particularly at low sequencing depth.