CRISPR RGEN Tools

BE-Analyzer

A JavaScript-based instant assessment tool for NGS data of CRISPR base edited cells.

Thanks to the improvements in the newest JavaScript engines in the most recent web browsers, the JavaScript based internal algorithm of BE-Analyzer completely runs on the client-side so that large amounts of sequencing data do not need to be uploaded to the server.

Citation info: Hwang G-H et al. Web-based design and analysis tools for CRISPR base editing. BMC Bioinformatics 19, 542 (2018).

To comfirm that the substitutions are derived from CRISPR base editors, it is recommended to compare the treated data with untreated one as a negative control.

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

Sequencing Data

File Type:

Read 1 (fastq or gzipped fastq):

Read 2 (fastq or gzipped fastq):

Control Data (optional)

File Type:

Read 1 (fastq or gzipped fastq):

Read 2 (fastq or gzipped fastq):

Basic Information

Full reference sequence (5' to 3'):

PAM Type:

Base editing type:

Base editing window

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

Note that reference sequences can be adjusted according to the direction of crRNA. If your crRNA targets the opposite strand of reference sequences, they will be displayed as reverse complementary form.

Reference

Komor AC et al., Nature 533, 420-424 (2016).
Kim YB et al., Nature Biotechnology 35, 371-376 (2017).
Nishida K et al., Science 353, aaf8729 (2016).
Nicole MG et al., Nature 551, 464-471 (2017).

Analysis Parameters

Additional flanking window for the analysis of CRISPR base editing (R)

Minimum frequency (n) [?]

Comparison range (L)

BE-Analyzer is not compatible with Internet Explorer.
Please use a different browser, e.g. Chrome or Microsoft Edge.

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	Sequences that have at least one base substitutions	Sequences that have to conversions in target windows	to Substitution Rate (%)

Control (Optional)
Total Sequences	With both indicator sequences	More than minimum frequency	Wild Type	Insertions	Deletions	Sequences that have at least one base substitutions	Sequences that have to conversions in target windows	to Substitution Rate (%)

Substitution Table

Analysis Results

Total Subsitution

to substitution in target windows

Substitution patterns of outcome

(Optional) Substitution patterns of control data

Sequence Information

Filtering by Sequence[?]

Count:

Base Edited Data
Control Data

ID	Sequence	Length	Count	Type
No entries found.

ID	Sequence	Length	Count	Type
No entries found.

BE-Analyzer

A JavaScript-based instant assessment tool for NGS data of CRISPR base edited cells.

Base edited data

Control data