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Old 06-29-2018, 04:47 AM   #1
Kaizen
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Default How to add GFP sequence to mouse genome for mapping

Hi guys,
I was wandering what is the right way to add the sequence of GFP reporter to a mouse genom. Basically instead of "geneA" in the genome the modified mouse has "geneA-IRES-GFP".
I guess that adding just the sequence of GFP as an extra chromosome is not ideal, since a read that would map to both "geneA" and "IRES-GFP" would not be mapped by STAR.
Does anyone know what to do?
Thanks
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Old 07-11-2018, 01:37 PM   #2
atpoint
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You could make an alternative genome by masking the exons of geneA in the fasta (so adding N instead of the actual sequence), and then add the transgene sequence as an extra chromosome.
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