How to create a custom reference genome and annotation?

Question

[soda]

I knock in a tag or some other sequence in one gene's c-terminal with CRISPR. Then I do a RNA-seq. My question is: how can I calculate the knock in's counts? May be I need to add the sequence to reference genome and modify my annotation file. So could you give me some advice? I can't use code to present my thoughts

[GenoMax]

What is the knock-in expected to do? Increase the size of the transcript? What would be the size of the new transcript compared to WT? If you are using something like salmon with the transcriptome, you could add another entry for the knock-in transcript and count.