Calculating deletion frequency (het/hom)

[olu2016]

Hi,

Would any of these two crispressopooled outputs (Alleles_frequency_table_around_sgRNA_XXXXX,txt or Alleles_frequency_table.txt) would be the ideal for inferring deletion frequency (het/hom)?

Thanks

[Colelyman]

Hi @olu2016,

Good question, if you are only interested in looking at deletion frequency you can use the --ignore_substitutions and --ignore_insertions parameters and then only deletions inside the quantification window will be counted in the editing rate.

Another way that you could do it is by specifying the --expected_hdr_amplicon_seq, then CRISPResso will classify the reads that have the deletion accordingly.

Let me know if this answers your question or if you are referring to something else!

Thanks,
Cole

[olu2016]

Hi @Colelyman,

Thanks for your explanation and information. It helps!