CRISPRessoAggregate error

[jleehan]

Hello!

I'm trying to use CRISPRessoAggregate on a couple of CRISPRessoPooled runs and I am getting an error that I'm uncertain how to fix.

When I input the following command:

CRISPRessoAggregate --name "Sample_Number" --prefix path/to/CRISPRessoPooled/directories/

I receive the following output:

ERROR: 'Namespace' object has no attribute 'verbosity'

I get the feeling that I'm not correctly assigning the --prefix option, but I'm not sure how exactly I'm messing this up.

Could anyone possibly help me troubleshoot this issue?

Thanks!

[Colelyman]

Hi @jleehan,

Thanks for using CRISPResso and sorry to hear that you are having trouble. This is not anything that you are doing wrong, but rather a bug (that I introduced 😬). There is a fix for this bug in master, but it hasn't been released into the conda package yet.

If you are comfortable with installing CRISPResso from source, you can get the fix before we make the conda release. How you do it is clone the repo, navigate into the repo, and then run pip install .. If you do this in the same environment that you had CRISPResso previously installed then you most likely won't run into any issues with installing the dependencies.

Good luck,
Cole

[jleehan]

I'm specifically interested in how to use the alignment viewer that's featured in supplementary figure 9. I don't know how to find the relevant data or images in the html reports (though it's possible it's not generated for CRISPRessoPooled which is the function I'm using for my samples). I definitely want to at least figure out how to use that specific function, but I'd also love to be able to access that in aggregate or compare so I could look at that kind of figure across samples fairly easily.

[Colelyman]

Good question, figure 9 is what we call the allele plot and it is generated by CRISPResso (you can see another example of it at the bottom of this page http://crispresso.pinellolab.org/static/demo/CRISPResso_on_allele_specific/CRISPResso2_report.html). When running CRISPRessoPooled, there won't be an allele plot on the main "summary" page because these figures summarize data across your samples, but if you navigate into the sub reports (the boxes with your sample names at the top of the summary report), you should be able to find the allele plot for each sample. Does that make sense?

[jleehan]

That makes sense, is there a specific argument or option that I need to include for the allele plot to be made? I can't seem to find the allele plot specifically when exploring the html reports. I tried adding the --write_detailed_allele_plot and --expand_allele_plots_by_quantification arguments together and separately and I can still never actually find that type of figure or where the data for that figure would be drawn from.

Edit: I looked at the report you linked and I noticed the big difference between my input and the one listed is the --write_cleaned_report option and the inclusion of the protospacer sequence with the -g option. Are these the options needed to get that allele plot in the report?

[kclem]

Right - plot 9 is only generated when you provide the spacer sequence with -g.

[jleehan]

Thank you, that's super helpful!