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akikuno / DAJIN

One-step genotyping software using a long-read sequencer
https://doi.org/10.1371/journal.pbio.3001507
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Genomes, number of sgRNAs #45

Closed amv33576 closed 2 years ago

amv33576 commented 3 years ago

Hello, Some questions about implementation:

  1. Can you use this software with other genomes?
  2. Is it possible to input more than one sgRNA? We used the https://ice.synthego.com/#/ with our sanger sequences.

I have an amplicon nanopore sequencing from insect genomes after mosaic CRISPR knockouts. the genomes are not in UCSC. I will really like to try your software on my data.

Best,

Anyi

akikuno commented 2 years ago

Hello, Anyi,

Sorry for the late reply and Thank you for your message.

  1. Currently, DAJIN can analyze only animals with UCSC references. We are planning to update and include organisms without UCSC references.

  2. Multiple sgRNAs can be applicable. Since the current DAJIN requires two alleles (wt and target), please create an arbitral target allele as shown below in the case of 1 cut deletion.

>wt
ACGTACGT
>target
ACGTAACGT

Sincerely,

Kuno