CRISPRnano manual
CRISPRnano v2 is a JavaScript-based program that was developed for rapid deep sequencing-based genotyping of nuclease edited cell clones. CRISPRnano supports noisy Oxford Nanopore but also Next Generation Sequencing (NGS) data such as Illumina, PacBio, or classic Sanger Sequencing.
Detailed manual illustration in the pdf file below
Input data:
CRISPRnano webserver analyzes FASTQ output files from ONT, NGS, PacBio or Sanger systems.
It analyzes multiple samples and currently supports up to 96 FASTQ files at the time.
Please(!), make sure that the correct fils order is applied in the file browser.
The file allocation to individual pie charts can be verified by the filename given at alignment track.
Data type:
Dependant on the sequencing datatype, the website will re-update the default parameters optimized for each datatype
Reference sequences, Gene name and gRNA
The reference sequence can be fetched from the genename (GENE SYMBOL in ENSEMBL) automatically. The recommended gRNA will be load when the genename is given.
If you want to use your customized reference, please leave the Gene Name blank.
Nuclease Target Site/gRNA
The Nuclease Target site/gRNA is briefly checked if it is located within the reference genome.
Interested region
For ONT reads, it is recommended to use 90 bp predicted DNA lesion. Larger regions are prone to false positive indels.
Larger regions (total of 100-160 bp) can be safely used with Illumina reads.
Targeting mutagenesis oligonucleotide
Donor oligonucleotide sequence is used to introduce a site-specific genomic modification.
Indel Threshold
The Indel Threshold percentage determines at what relative occurrence an individual indel mutation is considered as a unique allele of the respective clone analyzed, and is thus displayed in the alignment list.
Low threshold values can result in false positive allele calling due to sequencing errors,
whereas high threshold values result in false negative allele calling. Values in between 0 - 100 % can be entered. We recommend using 5% for ONT reads and 2% for Illumina reads (the default is set to 5%).
Full manual:
