After discussion of the first set of benchmarking results, we have decided to focus in on alevin-fry and explore more of the options available within alevin-fry. Specifically, the application of using the splici index with single-cell samples and use of the cr-like resolution strategy.
We also are going to add 2 more single nuclei RNA seq samples to the analysis to have a total of 4 single nuclei samples in our cohort for benchmarking.
Based on our discussion, we will be solely using the --unfiltered-pl option followed by additional filtering with emptyDrops. The following conditions (all using alevin-fry-unfiltered) will be tested and added to benchmarking:
sketch-full
sketch-cr-like*
sketch-cr-like w/splici index (single cell samples only)*
Tools indicated with a * will need to be applied to all samples in our benchmarking set (including the 2 new single nuclei samples) as this is the first time we are using these combinations. Additionally, we will need to run cellranger on the 2 new single nuclei samples.
After discussion of the first set of benchmarking results, we have decided to focus in on alevin-fry and explore more of the options available within alevin-fry. Specifically, the application of using the
spliciindex with single-cell samples and use of thecr-likeresolution strategy.We also are going to add 2 more single nuclei RNA seq samples to the analysis to have a total of 4 single nuclei samples in our cohort for benchmarking.
Based on our discussion, we will be solely using the
--unfiltered-ploption followed by additional filtering withemptyDrops. The following conditions (all using alevin-fry-unfiltered) will be tested and added to benchmarking:Tools indicated with a * will need to be applied to all samples in our benchmarking set (including the 2 new single nuclei samples) as this is the first time we are using these combinations. Additionally, we will need to run cellranger on the 2 new single nuclei samples.