CRISPResso mapping reads to wrong allele

[GreenSeaBug]

Hello,

I have three reference alleles (distinguished by several SNPs) and three reads. Except for edits at the canonical cut site, each read matches its respective allele (no N's). Yet, CRISPResso2 maps one of the reads to the wrong allele. How to figure out what is going wrong?

Thank you.

[Colelyman]

Hi @GreenSeaBug,

Are you able to provide the sequences? Also, are the alleles different even when there are edits at the cut site?

Thanks,
Cole

[GreenSeaBug]

Hi Cole,

Yes the sequences are different even when there are edits at the cut site. I have provided the sequences via email.

Thank you.

[Colelyman]

I haven't seen the email come through, could you send it to support@edilytics.com please?

[GreenSeaBug]

Sorry about that. OK, I have sent it to the email address you provided.

Thank you.

[GreenSeaBug]

Hi Cole,

Just wondering if you had a chance to look at this?

[Colelyman]

Apologies for the delay in response! I have responded to your email with the specifics, but for the sake of the public record the issue had to deal with the differences between the --amplicon_min_alignment_score and --default_min_aln_score.

For clarification, --default_min_aln_score only takes a single number (the default is 60), but --amplicon_min_alignment_score allows you to provide a comma separated list of values that correspond to each amplicon. For example, if you have the command

CRISPResso -a ACT...,GGG...,CCTATT...,TTTT... -an amp1,amp2,amp3,amp4 --amplicon_min_alignment_score 10,20,30,40

then amp1 will have a minimum alignment score of 10, amp2 will have 20, amp3 will have 30 and amp4 will have 40.