Finding chimeric reads for CRISPR edited mouse cells from RNA-Seq data

Question

[Ethan]

Hi, I am fairly new to doing RNA-Seq analysis. I am trying to find a way to visualize/analyze the efficiency of incorporating a human gene into the mouse genome using CRISPR. I have RNA-Seq data but am trying to develop a pipeline to see individual reads to see how successful the human gene is being incorporated into the mouse genome. What I would like to do is have the data aligned to the chimeric gene which has the mouse promoter and the human gene after because that is what the experiment is designed to do and see if the whole human gene is there, or certain parts are being incorporated more than others. Any help would be appreciated.

[Haci]

I would i) construct a custom genome representing your modifications, ii) a custom annotation file representing your modifications, iii) align to the new genome using the new annotations and iv) manaully inspect alignments at the site(s) of interest. reform seems to be developed for parts i and ii above, though I have not used it.