Question: How can I modify STAR alignment parameters in Cell Ranger?
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. 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.
Product: Single Cell Gene Expression, Single Cell Multiome ATAC + Gene Expression, Single Cell Immune Profiling
Last updated: July 2024