Fig. 1

SEESAW is a suite of tools for analysis of allelic imbalance across samples, first performing quantification and then statistical inference. A Salmon is used to quantify single-end (SE) or paired-end (PE) reads over a diploid transcriptome, and then estimates may be aggregated to various levels of resolution: isoform, TSS, or gene level. Different types of reads provide different types of information: PE1 contains both allelic and isoform-level information, PE2 contains only isoform-level information, and PE3 contains only allelic information. Information from all of these types of read data is included in quantification with Salmon. B Swish is then used to perform statistical testing of allelic imbalance across samples, taking into account multiple inferential replicates per sample (shown as boxes). Swish can test for global allelic imbalance, or differential or dynamic imbalance with respect to categorical or continuous covariates, respectively