If I remember correctly, your data are from some kind of scRNA-seq. Our default cutoffs were picked with typical (Illumina) bulk RNA-seq experiments in mind. I suspect that patterns for signal vs noise with your platform and sequencing depth might be quite different than bulk (or other single-cell platforms).
This is to say, without more information, I wouldn’t necessarily use the default parameters conclude that you can’t use your data to infer its presence – it’s not clear that the defaults are appropriate for your use case. The more replicate data you have with it relatively consistently there with counts comparable or large vs other junctions you are confident are there (especially considering/adjusting for any platform-specific biases), and doesn’t pick up too many other denovo junctions that you don’t have other reasons to believe in. In other words, from the splicegraph/majiq build side of things, you need to determine what the optimal thresholds are for your data.
P.S. I don’t remember how exact Cre-Lox recombination is with the sites of the deletion, but keep in mind that MAJIQ will treat denovo junctions with different coordinates independently. If you care that it happened but not necessarily the exact coordinates, there might be some benefit to pooling evidence.
P.P.S. this is definitely outside of the usual use case of MAJIQ since you are trying to use RNA-seq to infer the presence of a genomic deletion – not really splicing
P.P.P.S. if your aligner calls both splits (cigar op N) and deletions (cigar op D), note that MAJIQ only calls the N operations as junctions
Joseph Aicher (he/him/his)
MD/PhD Candidate, GS6
Perelman School of Medicine
Genomics and Computational Biology Graduate Group
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