As we are narrowing in on the choice of configuration for alevin-fry, we have yet to test use of the cr-like-em resolution that is one of the resolutions recommended for use with the splici index and with USA mode. We should compare the cr-like-em method to cr-like alone, with the only difference being that cr-like-em resolves multi-mapped reads using the expectation maximization algorithm, while cr-like discards those reads.
For this test, we will use 2 single-cell samples (SCPCR000126 and SCPCR000127) and 2 single-nuclei samples (SCPCR000220 and SCPCR000221). These samples will be run with the updated version of alevin-fry using salign, splici, and either cr-like-em or cr-like.
As we are narrowing in on the choice of configuration for alevin-fry, we have yet to test use of the
cr-like-emresolution that is one of the resolutions recommended for use with thespliciindex and with USA mode. We should compare thecr-like-emmethod tocr-likealone, with the only difference being thatcr-like-emresolves multi-mapped reads using the expectation maximization algorithm, whilecr-likediscards those reads.For this test, we will use 2 single-cell samples (SCPCR000126 and SCPCR000127) and 2 single-nuclei samples (SCPCR000220 and SCPCR000221). These samples will be run with the updated version of alevin-fry using
salign,splici, and eithercr-like-emorcr-like.