About visualization

[zwfsnowdream]

Thank you very much for developing CRISPResso2, such a powerful tool. I would like to analyze the mutation profile—particularly base substitutions—across the entire read (150 bp) aligned to the reference amplicon, rather than focusing solely on the sgRNA region. Could you please advise how to obtain this information from the visualization results? Thank you!

[kclem]

Hi @zwfsnowdream,
You can use the --plot_window_size parameter to increase the plot window size from 20bp (default) to however much of the amplicon you'd like to see. Note that setting this parameter to 50 will plot 50bp on either side of the guide cut site.

If you also want to visualize alleles without rerunning CRISPResso you can also check out this plotting helper script that allows you to plot asymmetrical plots not centered at the guide cut site: https://github.com/pinellolab/CRISPResso2/blob/master/scripts/plotCustomAllelePlot.py

[zwfsnowdream]

"Thank you very much for your answer. I have one more question—do you know the current progress of CRISPResso2 in analyzing third-generation sequencing results (such as ONT)?"

[kclem]

We're still working on this - and will let you know as soon as it's available.