Krzysztof Polanski
Krzysztof Polanski
Ran into this by proxy today via muon. Dropping a line in here so I'm up to date with developments on the matter.
Does normalisation imply dividing by the length of the sequence? If so, then that puts us pretty close to what Dandelion does, no?
I think we're all talking about slightly different things. If we take the Hamming distance and divide it by sequence length, we'll obtain a "percent of mismatches" measure, which is...
Another signal boost post. I just tried to analyse some BCR, so I mimicked the TCR tutorial.
Having had a chat with a biologist, I believe Scirpy's existing functionality covers BCR-specific phenomena (non-identity CDR3 comparisons for somatic hypermutation, and `.obs['..._c_gene']` for class-switch recombination). As such, it should...
Huh, weird. Having missed this insight in the paper, I ended up doing a computational experiment of my own to try to test the limits, and got less encouraging findings....
Thanks for all the insight, I'll try it without the common variants remap skipping. The person who pointed me at the samples says that they're from different individuals.
False alarm. The collaborator messed up the metadata and I was merging two samples for the same individual. I'm getting a lot more sensible results, even with `--common_variants`, once I...
I never reported back with findings, this might be of use to you. I took a ~3000-cell sample from one individual, and mixed in decreasing numbers of cells from a...
I can confirm I saw something similar, and adding `-B $PWD` to the singularity call somehow made it go away.