Finding cre recombinase in RNA-Seq reads

Question

[Greg P]

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

1. Is it feasible to find the sequence of the cre recombinase in the RNA-Seq reads (FASTQ files)?
2. If so, how could this be done?

[GenoMax]

While @harold.smith.tarheel's grep method may work to give you a quick yay/nay indication, you may want to take the cre sequence, create a quick index with an aligner of your choice and align.

[LionisOne]

@harold.smith.tarheel Hi Harold, could you tell me clearly how to find my Cre gene expression in Fastq file (better if you provide some example code) Thanks in advance

[Ram]

Do not add answers unless you're answering the top level question. Use Add Comment or Add Reply instead. I've moved your post to a comment on the top level post for now, but please be more careful in the future.

Answer 1

[harold.smith.tarheel]

1. If the gene that contains cre is transcribed, then yes.

2. It's as simple as searching the FASTQs for the 5' or 3' sequence of the cre transgene (e.g., using grep).