How to make allele frquency table for non-CRISPR data?

[sarakn97]

Hello,

I always use CRISPResso2 to analyze out CRISPR-editing efficiency. I love the allele frequency tables that show the variant reads and their frequencies.

I am now analyzing amplicon-seq data that was run for non-CRISPR data. The amplicons sequencing is targeted around a 220 bp region. I would love to make a table similar to the Crispresso2 allele frequency table for my data to see the different alleles within this small region.

Are there any packages for analyzing this type of data and producing the desired chart? Most amplicon-sequencing is done to analyze CRISPR-edited regions or microbiome data and I can't find any packages to get my desired results.

[Colelyman]

Happy to hear that CRISPResso2 is working well for you! The allele frequency table is custom designed in CRISPResso2, so I don't think that you will find a package to generate the same figure.

Have you by chance tried running your data through CRISPResso2 to see how it works? If running via the command line you could try using the --auto parameter so that you don't need to provide an amplicon or guide. If the issue is that you want to look at the entire 220 bp region, have a look at plotCustomAllelePlot.py which gives you more flexibility in the allele table plot after you have a CRISPResso2 run.