Quantification of editing frequency

[ChristinaKriaridou]

Hello,

I am using Crispresso to quantify the editing frequency of different genes.
For one of my genes (for a control individual) I can see in the "CRISPResso_quantification_of_editing_frequency.txt" file that Modified% is 8.25% and from the 17 reads that are modified 6 are only insertions, 10 are only deletions and 1 is insertion and deletion.
All of the 17 reads, except from 1, are single base pair deletions/insertions. These could be sequencing errors especially as they appear as single reads with deletions/insertions in different positions. For example an insertion like this GG->GGG.

Is there a way to remove these single base pair deletions/insertions from the quantification table?

Thank you very much for your help and time!

Cheers,
Christina

[Colelyman]

Hi @ChristinaKriaridou,

Thank you for using CRISPResso! I can think of a few ways of handling this, and which one you choose will depend on your context.

1. You can explicitly ignore all insertions with the --ignore_insertions parameter and ignore all deletions with the --ignore_deletions parameter within the quantification window.
2. You can also adjust your quantification window. If you are unsure what your quantification window is, you can provide the parameters that you used to run CRISPResso and we can help you figure that out. Here are a few ways that you can adjust the quantification window:
   2.a. Assuming that you provide the sgRNA sequence, you can use --quantification_window_center to adjust where the quantification will be centered according to the end of the guide. As well as --quantification_window_size to adjust how large the window is.
   2.b. If you don't provide the guide sequence, you can manually set the quantification window using `--quantification_window_coordinates.

I hope that this is helpful, and will allow you to refine your quantification. If you have tried the above, and the presumed sequencing errors are happening within the quantification window, those will have to be filtered as a post-processing step.

Please let us know if you have any additional questions or need any other help!

Thanks,
Cole