RNA-seq

[nikbaya]

Would it be possible to adapt this to confirm KOs using RNA-seq data?

[kclem]

Hi @nikbaya,

Could you provide a little more information on what you are hoping to use CRISPResso to do?

CRISPResso can analyze genomic sequencing at CRISPR targets to determine DNA changes resulting from CRISPR editing. If you have RNA reads aligned to the genome, these could probably be used to measure editing rates in transcripts using CRISPRessoWGS. However, you should consider that the results may not reflect editing on a DNA level because the CRISPR editing may affect transcription rates (e.g. if unedited genes are expressed higher than edited genes unedited RNA reads will be more prevalent in your RNA data).

However, CRISPResso isn't designed to analyze RNA expression. For this, I'd recommend something like DESeq2 to measure expression changes e.g. if a gene is knocked out when comparing a treated and control sample.