Is there a way to relax filter in refineTagsAndSort step?

[zthoms]

Wondering if there are any options to relax the filtering step in the refineTagsAndSort step?

I've been testing out both the "generic-ht-single-cell-amplicon-with-umi" workflow and the "generic-ht-single-cell-amplicon". When the pipeline considers UMIs, a significant portion of clones are getting tossed. When using the workflow that doesn't consider UMIs, we gain about 10% of T cells have paired TRA/TRB, and gain about 30% of T cells have at least TRA or TRB. We do gain some clones associated with non-T cells so background signal does increase (~5-10%) when the workflow that doesn't take UMIs into account.

Would be great to find some middle ground, so wondering if there are any tweaks that I can make to the refineTagsAndSort step in the "generic-ht-single-cell-amplicon-with-umi" workflow. Thanks!

[mizraelson]

It’s hard to say without investigating the data directly. There are multiple parameters that were tuned to work for the majority of cases. If the reports indicate where exactly the loss occurs, it might be possible to lower some thresholds. However, there is no one-size-fits-all solution.