I am analyzing some RNA-Seq data from mice that have a conditional knockout of a certain gene using the Lox-cre system. I am told, however, that the cre recombinase was accidentally placed inside the exon of a gene. I have two questions
- Is it feasible to find the sequence of the cre recombinase in the RNA-Seq reads (FASTQ files)?
- If so, how could this be done?