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Finding cre recombinase in RNA-Seq reads

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?
rna-seq
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updated by LionisOne • LionisOne • written by Greg P Greg P

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.

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written by GenoMax GenoMax

@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

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written by LionisOne • LionisOne

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.

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written by Ram Ram

1 answer

  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).

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written by harold.smith.tarheel harold.smith.tarheel

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