CRISPResso2

Analysis of genome editing outcomes from deep sequencing data

CRISPResso2 run information

Data: Mapping statistics

CRISPResso version: 2.0.40

Run completed: 2020-07-10 00:38:58

Amplicon sequence:

ACGTCTCATATGCCCCTTGGCAGTCATCTTAGTCATTACCTGAGGTGTTCGTTGTAACTCATATAAACTGAGTTCCCATGTTTTGCTTAATGGTTGAGTTCCGTTTGTCTGCACAGCCTGAGACATTGCTGGAAATAAAGAAGAGAGAAAAACAATTTTAGTATTTGGAAGGGAAGTGCTATGGTCTGAATGTATGTGTCCCACCAAAATTCCTACGT

Command used:

CRISPResso --fastq_r1 prime_editor.fastq.gz --amplicon_seq ACGTCTCATATGCCCCTTGGCAGTCATCTTAGTCATTACCTGAGGTGTTCGTTGTAACTCATATAAACTGAGTTCCCATGTTTTGCTTAATGGTTGAGTTCCGTTTGTCTGCACAGCCTGAGACATTGCTGGAAATAAAGAAGAGAGAAAAACAATTTTAGTATTTGGAAGGGAAGTGCTATGGTCTGAATGTATGTGTCCCACCAAAATTCCTACGT --prime_editing_pegRNA_spacer_seq GTCATCTTAGTCATTACCTG --prime_editing_pegRNA_extension_seq AACGAACACCTCATGTAATGACTAAGATG --prime_editing_nicking_guide_seq CTCAACCATTAAGCAAAACAT --prime_editing_pegRNA_scaffold_seq GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC --write_cleaned_report --place_report_in_output_folder

Parameters:

allele_plot_pcts_only_for_assigned_reference: False
aln_seed_count: 5
aln_seed_len: 10
aln_seed_min: 2
amplicon_min_alignment_score: 
amplicon_name: Reference
amplicon_seq: ACGTCTCATATGCCCCTTGGCAGTCATCTTAGTCATTACCTGAGGTGTTCGTTGTAACTCATATAAACTGAGTTCCCATGTTTTGCTTAATGGTTGAGTTCCGTTTGTCTGCACAGCCTGAGACATTGCTGGAAATAAAGAAGAGAGAAAAACAATTTTAGTATTTGGAAGGGAAGTGCTATGGTCTGAATGTATGTGTCCCACCAAAATTCCTACGT
annotate_wildtype_allele: 
auto: False
bam_chr_loc: 
bam_input: 
base_editor_output: False
coding_seq: 
conversion_nuc_from: C
conversion_nuc_to: T
crispresso1_mode: False
debug: False
default_min_aln_score: 60
discard_indel_reads: False
dsODN: 
dump: False
exclude_bp_from_left: 15
exclude_bp_from_right: 15
expand_allele_plots_by_quantification: False
expand_ambiguous_alignments: False
expected_hdr_amplicon_seq: 
fastq_r1: prime_editor.fastq.gz
fastq_r2: 
file_prefix: 
flash_command: flash
flexiguide_homology: 80
flexiguide_name: 
flexiguide_seq: None
force_merge_pairs: False
guide_name: 
guide_seq: 
ignore_deletions: False
ignore_insertions: False
ignore_substitutions: False
keep_intermediate: False
max_paired_end_reads_overlap: 100
max_rows_alleles_around_cut_to_plot: 50
min_average_read_quality: 0
min_bp_quality_or_N: 0
min_frequency_alleles_around_cut_to_plot: 0.2
min_paired_end_reads_overlap: 10
min_single_bp_quality: 0
name: 
needleman_wunsch_aln_matrix_loc: EDNAFULL
needleman_wunsch_gap_extend: -2
needleman_wunsch_gap_incentive: 1
needleman_wunsch_gap_open: -20
no_rerun: False
output_folder: 
place_report_in_output_folder: True
plot_window_size: 20
prime_editing_nicking_guide_seq: CTCAACCATTAAGCAAAACAT
prime_editing_pegRNA_extension_quantification_window_size: 5
prime_editing_pegRNA_extension_seq: AACGAACACCTCATGTAATGACTAAGATG
prime_editing_pegRNA_scaffold_min_match_length: 1
prime_editing_pegRNA_scaffold_seq: GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC
prime_editing_pegRNA_spacer_seq: GTCATCTTAGTCATTACCTG
quantification_window_center: -3
quantification_window_coordinates: None
quantification_window_size: 1
save_also_png: False
split_interleaved_input: False
stringent_flash_merging: False
suppress_plots: False
suppress_report: False
trim_sequences: False
trimmomatic_command: trimmomatic
trimmomatic_options_string: 
write_cleaned_report: True
write_detailed_allele_table: False

Running log

Allele assignments

Data: Quantification of editing

Data: Quantification of editing

Prime editing report (all reads aligned to Reference)

Data: Nucleotide frequency table for Reference

Data: Nucleotide frequency table for Prime-edited

Data: Nucleotide frequency table for Scaffold-incorporated

Prime editing summary plots at analysis positions (aligned to Reference)
Scaffold insertions

Data: Scaffold insertion alleles with insertion sizes

Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below: