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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 .

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