Data: Mapping statistics
CRISPResso version: 2.0.40
Run completed: 2020-07-10 00:35:39
Amplicon sequence:
CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCACTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG,CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCCCTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG
Guide sequence:
GTGCGGAGCCACTTCGAGCAGC
Command used:
CRISPResso -r1 allele_specific.fastq.gz -a CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCACTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG,CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCCCTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG -an P23H,WT -g GTGCGGAGCCACTTCGAGCAGC --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: P23H,WT amplicon_seq: CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCACTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG,CGAGAGCCGCAGCCATGAACGGCACAGAGGGCCCCAATTTTTATGTGCCCTTCTCCAACGTCACAGGCGTGGTGCGGAGCCCCTTCGAGCAGCCGCAGTACTACCTGGCGGAACCATGGCAGTTCTCCATGCTGGCAGCGTACATGTTCCTGCTCATCGTGCTGGG 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: allele_specific.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: GTGCGGAGCCACTTCGAGCAGC 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: prime_editing_pegRNA_extension_quantification_window_size: 5 prime_editing_pegRNA_extension_seq: prime_editing_pegRNA_scaffold_min_match_length: 1 prime_editing_pegRNA_scaffold_seq: prime_editing_pegRNA_spacer_seq: 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
Reads are aligned to each amplicon sequence separately. Quantification and visualization of these reads are shown for each amplicon below: