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hi we have transgenic mice with human gene inserted. if we profom rnaseq for the mice, how can we get the expression value of the human gene inserted to the mice? and use this expression to compare with other mice gene expression?

the mice ref genome doesn't have this piece of human gene sequence. anybody knows how?

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You will need to create (and probably index) a "custom" genome/transcriptome, mouse + whatever human genes inserted, depending on the alignment method of choice. And how to do so would depend on the your tool of choice.

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