Question: Why am I receiving the barcode compatibility error and how to resolve this ?
Barcodes from the [Gene Expression] library and the [Antibody Capture] library have insufficient overlap.Answer:
Matched Gene Expression and Antibody Capture libraries are expected to have high overlap of 10x barcodes. This error message occurs when there isn't sufficient overlap of the barcodes. Following are some common reasons for this issue:
- (Most common case) Mismatch in samples between the Antibody and Gene Expression libraries.
- The quality of R1 reads is low. You can check the read quality with FastQC (FASTQC KB article).
- Very few Ab reads (for example less than 10,000 reads).
- Poor quality of Antibody library (such as high Antibody aggregation).
If none of the aforementioned scenarios are relevant to your datasets, this error can be resolved by implementing one of the solutions below, according to the Cell Ranger version in use.
Method 1:
If using Cell Ranger v7 and above, the resolution involves a command-line option which can be set to false as discussed below:
- if you are using a
cellranger count, please add the parameter--check-library-compatibility=falsein the command-line. - If you are using
cellranger multipipeline you can bypass this check by addingcheck-library-compatibility,falseto the [gene-expression] section of your multi config CSV.
Method 2:
If using Cell Ranger v5 or v6, it is possible to tweak the parameters in the following file to get the analysis to complete.
cellranger-x.y.z/lib/bin/parameters.toml
Update the parameter value for "min_barcode_similarity" from 0.1 (below screenshot) to a value below the number displayed in your error message. Please revert to the default (0.1) after this set of samples are analyzed.
Note: For any other versions of Cell Ranger not explicitly outlined, it is recommended to upgrade to one of the above versions.
Products: Single Cell Gene Expression
Last updated: Dec 2023