| Method ID | Agreement | Strand-aware | Counting of multi-gene reads | Comments |
|---|---|---|---|---|
| alevin_sep_gtr | good | yes | yes | |
| alevin_coll_gtr | good | yes | yes | |
| kallisto|bus_sep_excl | good | no | no | Reads in ambiguous regions typically discarded |
| starsolo | good | yes | no | |
| alevin_coll_decoy_gtr | variable | yes | yes | |
| velocyto | variable | yes | no | |
| kallisto|bus_coll_excl | variable | no | no | |
| alevin_sep_decoy_gtr | poor | yes | yes | Reads in ambiguous regions double-counted. |
| alevin_spliced_unspliced_gtr | variable | yes | yes | 3’ tag protocols does not provide enough information for spliced/unspliced resolution. |
| dropest | poor | no | partially | Insufficient UMI collapsing |
| kallisto|bus_coll_incl | poor | no | no | |
| kallisto|bus_sep_incl | poor | no | no | Reads in ambiguous regions double-counted. |
| starsolo_diff | variable | yes | partially | Non-zero unspliced count possible even without introns; nominally negative unspliced count possible. |
Reference: Soneson C, Srivastava A, Patro R, Stadler MB. Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. PLoS Comput Biol. 2021 Jan 11;17(1):e1008585. doi: 10.1371/journal.pcbi.1008585. PMID: 33428615; PMCID: PMC7822509.