kclem
commented
1 month ago Hi @lpcv0309,
I'm sorry about the confusion.
Each row in CRISPResso_quantification_of_editing_frequency.txt provides statistics for a separate amplicon. The top row is the Reference(unedited) amplicon, and the second row is for the Prime-edited amplicon. The Unmodified % and Modified % columns show the percent of reads aligned to 'Reference' or 'Prime Edited' that were unmodified (or modified).
If you'd like to compute the values in the barplots/piecharts from the values in CRISPResso_quantification_of_editing_frequency.txt, simply divide the values in the Unmodified or Modified columns by the value in Reads_aligned_all_amplicons. E.g. to get the percent of all reads that were Reference Unmodified, the calculation is 2786/3240 = 0.8598765 (shown as 85.99 in the barplot above).
The tool CRISPRessoAggregate can be used to aggregate multiple runs and will produce a file for performing downstream statistical tests.
We don't plan on implementing any changes, but let us know if you need help with your downstream processing!
Describe the bug In the analysis results of the prime editor, 'Figure 1c: Alignment and editing frequency of reads as determined by the percentage and number of sequence reads showing unmodified and modified alleles.' The values for 'Reference Unmodified%, Reference Modified%, Prime-edited Unmodified%, Prime-edited Modified%' in the associated file 'CRISPResso_quantification_of_editing_frequency.txt' differ from the figures shown. Their sum is 200%, while the sum in bar or pie charts should only be 100%.
Expected behavior Modify the calculation rules for Unmodified% and Modified% in the 'CRISPResso_quantification_of_editing_frequency.txt' file to ensure the values match the figures shown. This will facilitate exporting the data and combining results from multiple replicates for replotting.
CRISPResso_quantification_of_editing_frequency.txt