CRISPResso2

Analysis of genome editing outcomes from deep sequencing data

CRISPResso2 run information

CRISPResso version: 2.0.25

Run completed: 2019-02-21 20:51:47

Amplicon sequence:

acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcatctgactcctgTggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggttggtatcaaggtta

Guide sequence:

TGCACCATGGTGTCTGTTTG

Command used:

CRISPResso -r1 hdr.fastq.gz -a acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcatctgactcctgTggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggttggtatcaaggtta -e acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcaCctgactccGgaggagaagtctgccgttactgcGctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggttggtatcaaggtta -c atggtgcatctgactcctgTggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcag -g TGCACCATGGTGTCTGTTTG --write_cleaned_report

Parameters:

aln_seed_count: 5
aln_seed_len: 10
aln_seed_min: 2
amplicon_min_alignment_score: 
amplicon_name: Reference
amplicon_seq: acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcatctgactcctgTggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggttggtatcaaggtta
auto: False
base_editor_output: False
coding_seq: atggtgcatctgactcctgTggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcag
conversion_nuc_from: C
conversion_nuc_to: T
crispresso1_mode: False
debug: False
default_min_aln_score: 60
discard_indel_reads: False
dump: False
exclude_bp_from_left: 15
exclude_bp_from_right: 15
expand_ambiguous_alignments: False
expected_hdr_amplicon_seq: acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcaCctgactccGgaggagaagtctgccgttactgcGctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggttggtatcaaggtta
fastq_r1: hdr.fastq.gz
fastq_r2: 
file_prefix: 
flash_command: flash
guide_seq: TGCACCATGGTGTCTGTTTG
ignore_deletions: False
ignore_insertions: False
ignore_substitutions: False
keep_intermediate: False
max_paired_end_reads_overlap: None
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: None
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: 
plot_window_size: 40
quantification_window_center: -3
quantification_window_coordinates: None
quantification_window_size: 1
save_also_png: False
split_paired_end: False
suppress_plots: False
suppress_report: False
trim_sequences: False
trimmomatic_command: trimmomatic
trimmomatic_options_string: 
write_cleaned_report: True

Allele assignments
Global frameshift analysis
Global frameshift mutagenesis profiles
Global splicing analysis

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

Amplicons