Hello,
I have some PacBio scRNA-Seq MAS-Isoseq data that I have been following the isoseq best practices to process/analyze. I wanted to try out Isosceles instead of Pigeon/SQANTI because I have multiple samples sequencesdseparately and having stable isoform identifiers to compare expression levels would be very helpful.
I'm curious what you would recommend for the initial data pre-processing step. The Isoseq workflow uses pbmm2 (minimap wrapper) and I'm not sure how that handles the --junc-bed flag. I'm leaning towards just trying with the mapped BAM from pbmm2 that has subsequently been deduplicated based on UMI.
Thanks!
Hello,
I have some PacBio scRNA-Seq MAS-Isoseq data that I have been following the isoseq best practices to process/analyze. I wanted to try out Isosceles instead of Pigeon/SQANTI because I have multiple samples sequencesdseparately and having stable isoform identifiers to compare expression levels would be very helpful.
I'm curious what you would recommend for the initial data pre-processing step. The Isoseq workflow uses pbmm2 (minimap wrapper) and I'm not sure how that handles the --junc-bed flag. I'm leaning towards just trying with the mapped BAM from pbmm2 that has subsequently been deduplicated based on UMI.
Thanks!