Not sure where to start?

Examples

NHEJ (Non-homologous end joining)
Multiple alleles
Base-editors
HDR (Homology directed repair)
Prime editing
Batch mode

CRISPResso2

Analysis of genome editing outcomes from deep sequencing data

Not sure where to start?

Examples

NHEJ (Non-homologous end joining)
Multiple alleles
Base-editors
HDR (Homology directed repair)
Prime editing
Batch mode

Experimental design

Editing tool:

Sequencing design:

Sample name

Fastq file R1

Use the Browse button or drag and drop a fastq or fastq.gz file here

Fastq file R2

Use the Browse button or drag and drop a fastq or fastq.gz file here

Amplicon

sgRNA

Sample name

Fastq file

" " + " Use the Browse button or drag and drop a fastq or fastq.gz file here " +

Amplicon

sgRNA

Optional parameters

Sample Name

Amplicon Name/s

Minimum homology for alignment to an amplicon:

50% 60% 70% 80% 90% 100%

Base editing

Base editor output

Base editor target base

A C T G

Base editor result base

A C T G

Prime editing

pegRNA spacer sequence

pegRNA extension sequence

pegRNA extension quantification window size:

1 5 10

Nicking sgRNA

Scaffold sequence

Quantification window

Center of the quantification window (relative to 3' end of the provided sgRNA):

-15 -10 -3 0 +1

Quantification window size (bp):

No window 1 2 3 4 5 6 7 8 9 10 15 20 25 30

Plot window size (bp):

5 10 20 30

Ignore substitutions

Ignore insertions

Ignore deletions

HDR

Expected HDR amplicon sequence:

Exon specification

Coding Sequence/s:

Quality filtering and trimming

Minimum average read quality (phred33 scale):

No Filter >10 >20 >30 >35

Minimum single bp quality (phred33 scale):

No Filter >10 >20 >30 >35

Replace bases with N that have a quality lower than (phred33 scale):

No Filter <10 <20 <30 <35

Exclude bp from the left side of the amplicon sequence for the quantification of the mutations:

Disabled 5 10 15 20 40 50

Exclude bp from the right side of the amplicon sequence for the quantification of the mutations:

Disabled 5 10 15 20 40 50

Trimming adapter:

No Trimming Nextera PE TruSeq3 PE TruSeq3 SE TruSeq2 PE TruSeq2 SE

By clicking the submit button, I agree to use CRISPResso2 in accordance with Partners' Terms and Conditions.

For analysis of amplicon pools, WGS data, and comparing multiple conditions, command line utilities for running CRISPResso2 on your machine or cluster are available at: https://github.com/pinellolab/CRISPResso2.

If you like CRISPResso2 please support us by citing it in your work:
Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L.
CRISPResso2 provides accurate and rapid genome editing sequence analysis.
Nat Biotechnol. 2019 Mar; 37(3):224-226. doi: 10.1038/s41587-019-0032-3. PubMed PMID: 30809026.

Tweet about CRISPresso2!

Not sure where to start?

Manual

Source on Github

Examples

CRISPResso2

Analysis of genome editing outcomes from deep sequencing data

Not sure where to start?

Manual

Source on Github

Examples

Experimental design

Editing tool:

Sequencing design:

Optional parameters

Base editing

Prime editing

Quantification window

HDR

Exon specification

Quality filtering and trimming