Question: How can I modify the default parameters in Cell Ranger in the count pipeline?
Answer: The default STAR parameters used in Cell Ranger are described here. Modifying the STAR alignment parameters is not supported by 10x Genomics. However, if needed, you can change the parameters for STAR alignment as described below.
If you are working with Cell Ranger 4+, you can edit the file cellranger-x.y.x/lib/bin/parameters.toml in your Cell Ranger installation. If you are working with Cell Ranger ARC, you can edit the file cellranger-arc-x.y.x/lib/bin/parameters.toml. One of the parameters in this file is "star_parameters", which by default is as below.
star_parameters = ""
You can input the parameters you would like in star_parameters = "". For example, here is what it would look like if you were to change two parameters
star_parameters=”--outFilterMismatchNmax=5 --outFilterMismatchNoverLmax=0.2”
If you are working with Cell Ranger 3 or less, unfortunately, there is no way to modify these parameters without editing the source code directly. The source code is included in the Cell Ranger software download and is also at https://github.com/10XGenomics/cellranger. The relevant code for alignment is here.
Source code for 10x pipelines is available on github.com for interested customers. However, we are not staffed to answer questions about it or provide support for modifications.
Product: Single Cell Gene Expression, Single Cell Multiome ATAC + Gene Expression, Single Cell Immune Profiling
Last updated: June 2023