IAOseq identifies the expression levels of overlapping genes from standard RNA-seq data based on reads distributions along the transcribed regions. The proposed computational pipeline is not restricted to the overlapping types and can also be applied to correct expression levels of same strand overlapping genes.
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BMC Bioinformatics. 2015;16(Suppl 1):S3. doi: 10.1186/1471-2105-16-S1-S3. Epub 2015 Jan 21.
IAOseq: inferring abundance of overlapping genes using RNA-seq data.
Sun H, Yang S, Tun L, Li Y.