CRISPResso2

Analysis of genome editing outcomes from deep sequencing data

CRISPResso2 run information

CRISPResso version: 2.0.10b

Run completed: 2018-09-21 21:52:00

Amplicon sequence:

GCCAAAAGAATGTCAACAGAAATCAGAACATAACACTAAGTAAGTTTAACATGTACTTTTATTAACAACTTAATACAAGACTGTACACTGTAGGTGCTGAAATCAACCCACTCCTGAAAACTGAAAAACCAGCATTTCTATACCACTTTGGGCTTTGGTTATAAGTGCCATCTTCTACAGCAAAATCACGTCTTAAGAACAGGAAAAACGTTCCACGGGAATGGAGAGATTATCTATGCATAAACAGCTGGGGATCATTT

Guide sequence:

AATACAAGACTGTACACTGT

Command used:

CRISPResso -a GCCAAAAGAATGTCAACAGAAATCAGAACATAACACTAAGTAAGTTTAACATGTACTTTTATTAACAACTTAATACAAGACTGTACACTGTAGGTGCTGAAATCAACCCACTCCTGAAAACTGAAAAACCAGCATTTCTATACCACTTTGGGCTTTGGTTATAAGTGCCATCTTCTACAGCAAAATCACGTCTTAAGAACAGGAAAAACGTTCCACGGGAATGGAGAGATTATCTATGCATAAACAGCTGGGGATCATTT -r1 CRISPResso_Input_Reads_3c14385e-ad3c-4cb2-9a06-ec16f8b9c589.gz -r2 CRISPResso_Input_Reads_094d3b3a-f85c-4d4e-873f-9dc3b6b0a884.gz -g AATACAAGACTGTACACTGT -q 0 -s 0 --min_bp_quality_or_N 0 --exclude_bp_from_left 15 --exclude_bp_from_right 15 --conversion_nuc_from C --conversion_nuc_to T -w 1 -wc -3 --name dlJzEa --output_folder CRISPRessoRundlJzEa --write_cleaned_report

Parameters:

aln_seed_count: 4
aln_seed_len: 6
aln_seed_min: 2
amplicon_min_alignment_score: 60
amplicon_name: Reference
amplicon_seq: GCCAAAAGAATGTCAACAGAAATCAGAACATAACACTAAGTAAGTTTAACATGTACTTTTATTAACAACTTAATACAAGACTGTACACTGTAGGTGCTGAAATCAACCCACTCCTGAAAACTGAAAAACCAGCATTTCTATACCACTTTGGGCTTTGGTTATAAGTGCCATCTTCTACAGCAAAATCACGTCTTAAGAACAGGAAAAACGTTCCACGGGAATGGAGAGATTATCTATGCATAAACAGCTGGGGATCATTT
auto: False
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
dump: False
exclude_bp_from_left: 15
exclude_bp_from_right: 15
expand_ambiguous_alignments: False
expected_hdr_amplicon_seq: 
fastq_r1: CRISPResso_Input_Reads_3c14385e-ad3c-4cb2-9a06-ec16f8b9c589.gz
fastq_r2: CRISPResso_Input_Reads_094d3b3a-f85c-4d4e-873f-9dc3b6b0a884.gz
file_prefix: 
guide_seq: AATACAAGACTGTACACTGT
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: 4
min_single_bp_quality: 0
name: dlJzEa
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: CRISPRessoRundlJzEa
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_report: False
trim_sequences: False
trimmomatic_options_string: NexteraPE-PE.fa:0:90:10:0:true MINLEN:40
write_cleaned_report: True

Allele assignments
Nucleotide composition
Modification lengths
Allele plots