Question: How do I modify the search distance of feature linkages in my multiome analysis?
Answer: By default, Cell Ranger ARC only looks for linkages within the same chromosome, and within 1 Mbp of the selected feature.
The pipeline does have a hidden parameter --feature-linkage-max-dist-mb that allows you to go beyond 1 Mbp. For example, if you run cellranger-arc count while specifying --feature-linkage-max-dist-mb=1.75, then the pipeline would look for linkages within 1.75 Mbp.
Please keep in mind that this parameter is kept hidden because the pipeline runtime, as well as the size of the resulting Loupe file, can grow very quickly. Please adjust the values conservatively and in small increments, otherwise the pipeline may fail to run to completion.
Note: This type of analysis is not officially supported. We do not recommend or advise the analysis of single modalities from the multiome assay. The main benefits of the multiome assay i.e. joint cell-calling and feature linkages will not be available when analysis is carried out in this way.