I have a library with co-processed GEX and antibody capture which I am attempting to process with "cellranger multi". It failes with the following error:
Barcodes from the [Gene Expression] library and the [Antibody Capture] library have insufficient overlap. This usually indicates a mismatched pair of libraries, i.e. they likely originated from different cells or samples and this error can usually be fixed by ensuring the provided FASTQ data were all generated from the same sample. The cosine similarity measure was calculated to be 0.0643, but the minimum similarity threshold is 0.1000
However, if I separately process the GEX and AC libraries, I find that of 1,103 GEX barcodes post filter and 1,148 AC barcodes post filter, 1,170 match. In the raw data, these numbers are 277,382, 733,782, and 276,862, respectively.
Is it possible to force cellranger to proceed past this step?
Hi,
I have a library with co-processed GEX and antibody capture which I am attempting to process with "cellranger multi". It failes with the following error:
Barcodes from the [Gene Expression] library and the [Antibody Capture] library have insufficient overlap. This usually indicates a mismatched pair of libraries, i.e. they likely originated from different cells or samples and this error can usually be fixed by ensuring the provided FASTQ data were all generated from the same sample. The cosine similarity measure was calculated to be 0.0643, but the minimum similarity threshold is 0.1000However, if I separately process the GEX and AC libraries, I find that of 1,103 GEX barcodes post filter and 1,148 AC barcodes post filter, 1,170 match. In the raw data, these numbers are 277,382, 733,782, and 276,862, respectively.
Is it possible to force cellranger to proceed past this step?
Thank you.