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pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
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ERROR：HDR number in the plot not the same as the number in txt file #448

Closed Masterchiefm closed 3 months ago

Masterchiefm commented 3 months ago

Describe the bug Hello, I think the line 1 number in plot "9.HDR.Alleles_frequency_table_around_sg.png" shoud be the same with the nuber in "CRISPResso_quantification_of_editing_frequency.txt"

However, the HDR nuber in plot is 55509 reads, while the HDR_unmodified in txt is 55662. Is it a bug or did I misunderstanding the meaning of the plot? Screenshot_20240624_232005

Screenshot_20240624_231426_cn wps moffice_eng

Expected behavior the HDR number should be the same in txt and plot.

kclem commented 3 months ago

Hi @Masterchiefm,

Thanks for using CRISPResso. I'm guessing the other alleles had low allele frequency, and the allele plot will only show alleles with a presence of greater than 0.2% If you would like to see other alleles, please set the parameters --min_frequency_alleles_around_cut_to_plot. Note that an additional parameter -max_rows_alleles_around_cut_to_plot sets the maximum number of rows plotted.

From the documentation: --min_frequency_alleles_around_cut_to_plot: Minimum % reads required to report an allele in the alleles table plot. This parameter only affects plotting. All alleles will be reported in data files. (default: 0.2 (i.e. 0.2%))

--max_rows_alleles_around_cut_to_plot: Maximum number of rows to report in the alleles table plot. (default: 50)

I hope that helps!

Masterchiefm commented 3 months ago

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