CRISPR RGEN Tools

CRISPR-Sub

A statistical assessment tool for Cas9-mediated substitutions in high-throughput sequencing data

High-throughput sequencing is the primary means of assessing indel and substitution frequencies in bulk populations of cells in the gene editing field. However, it is difficult to detect bona fide substitutions, which are embedded among experimentally-induced substitution errors, in high-throughput sequencing data. we developed a novel analysis method, named CRISPR-Sub, to statistically detect Cas9-mediated substitutions in high-throughput sequencing data by comparing Mock- and CRISPR-treated samples.

Citation info: Hwang G-H. et al. CRISPR-Sub: analysis of DNA substitution mutations caused by CRISPR-Cas9 in human cells. Computational and Structural Biotechnology Journal 18, 1686-1694 (2020).

Please input your data in below form, or download an example data here.

Download an off-line version of CRISPR-Sub here.

Sequencing Data
File Type:

Read 1 (fastq or gzipped fastq):

Read 2 (fastq or gzipped fastq):

Single Read File (fastq or gzipped fastq):

Control Data
File Type:

Read 1 (fastq or gzipped fastq):

Read 2 (fastq or gzipped fastq):

Single Read File (fastq or gzipped fastq):

Basic Information
Full reference sequence (5' to 3'):

PAM Type:

Select PAM:

Target DNA sequence (5' to 3', without PAM sequence):

Analysis Parameters
Comparison range(R)

Minimum frequency (n) [?]

Input Summary

WT sequence
(blue: indicator sequences at each ends of comparision range, green: crRNA sequence, red: WT marker sequence)

crRNA sequence

Comparison range (R) [?] Minimum frequency (n) [?]

Progress

CRISPR-treated data

Initializing...

Mock-treated data

Initializing...

Input Summary

WT sequence
(blue: indicator sequences at each ends of comparision range, green: crRNA sequence, red: WT marker sequence)

crRNA sequence

Target window (R) [?] Minimum frequency (n) [?]

Result Summary

Total Sequences With both indicator sequences More than minimum frequency Wild Type Insertions Deletions Indel Rate (%) Apparent Substitution Rate (%)

All queries WT-length group

Mock-treated

Total Sequences With both indicator sequences More than minimum frequency Wild Type Insertions Deletions Indel Rate (%) Apparent Substitution Rate (%)

All queries WT-length group

Analysis Results

Fold Scatter Plot

Fold Frequency

Hotspot Positions

Sequence Information

All

WTs

Substitutions

Insertions

Deletions

Base Edited Data

Control Data

ID Sequence Length Count Type

No entries found.

ID Sequence Length Count Type

No entries found.

WT sequence (blue: indicator sequences at each ends of comparision range, green: crRNA sequence, red: WT marker sequence)



crRNA sequence

Comparison range (R) [?]			Minimum frequency (n) [?]

WT sequence (blue: indicator sequences at each ends of comparision range, green: crRNA sequence, red: WT marker sequence)



crRNA sequence

Target window (R) [?]			Minimum frequency (n) [?]

Total Sequences	With both indicator sequences	More than minimum frequency	Wild Type	Insertions	Deletions	Indel Rate (%)	Apparent Substitution Rate (%)
Total Sequences	With both indicator sequences	More than minimum frequency	Wild Type	Insertions	Deletions	Indel Rate (%)	All queries	WT-length group

Mock-treated
Total Sequences	With both indicator sequences	More than minimum frequency	Wild Type	Insertions	Deletions	Indel Rate (%)	Apparent Substitution Rate (%)
Total Sequences	With both indicator sequences	More than minimum frequency	Wild Type	Insertions	Deletions	Indel Rate (%)	All queries	WT-length group