Base "N" in allele frequency quilts plot

[xguo-nveloptx]

N base This is more like a clarification or question, not exactly a bug. I notice that there are N in the allele frequency.txt output and the allele quilt plot. such as this one:

I am guessing that Crispressos clusters different insertions at the same place into one allele? But would appreciate if someone can clarify.

[kclem]

Hi @xguo-nveloptx,

The N in the allele frequency table comes from N's in your sequencing reads.

Insertions at the same location are not clustered. Each insertion will be present as a separate row in the allele frequency table, and the inserted bases are displayed in the table.

Does that make sense?

[xguo-nveloptx]

Thank you for clarification!

From: Kendell Clement @.> Date: Thursday, March 28, 2024 at 11:36 AM To: pinellolab/CRISPResso2 @.> Cc: Xiaoyun Guo @.>, Mention @.> Subject: Re: [pinellolab/CRISPResso2] Base "N" in allele frequency quilts plot (Issue #402) You don't often get email from @.*** Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

Hi @xguo-nveloptxhttps://github.com/xguo-nveloptx,

The N in the allele frequency table comes from N's in your sequencing reads.

Insertions at the same location are not clustered. Each insertion will be present as a separate row in the allele frequency table, and the inserted bases are displayed in the table.

Does that make sense?

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