CRISPRessoBatch
CRISPRessoBatch allows users to analyze multiple input files and other command line arguments by uploading a Batch file, and then to run CRISPResso2 analysis on each file in parallel. Samples for which the amplicon and guide sequences are the same will be compared between batches, producing useful summary tables and comparison plots.
CRISPRessoBatch Parameters
CRISPRessoBatch Examples
CRISPRessoBatch‑‑amplicon_seq ‑‑amplicon_name ‑‑amplicon_min_alignment_score ‑‑default_min_aln_score ‑‑expand_ambiguous_alignments ‑‑assign_ambiguous_alignments_to_first_reference ‑‑guide_seq ‑‑guide_name ‑‑flexiguide_seq ‑‑flexiguide_homology ‑‑flexiguide_name ‑‑flexiguide_gap_open_penalty ‑‑flexiguide_gap_extend_penalty ‑‑discard_guide_positions_overhanging_amplicon_edge ‑‑expected_hdr_amplicon_seq ‑‑coding_seq ‑‑config_file ‑‑min_average_read_quality ‑‑min_single_bp_quality ‑‑min_bp_quality_or_N ‑‑file_prefix ‑‑name ‑‑display_name ‑‑suppress_amplicon_name_truncation ‑‑output_folder ‑‑verbosity ‑‑split_interleaved_input ‑‑trim_sequences ‑‑trimmomatic_command ‑‑trimmomatic_options_string ‑‑flash_command ‑‑fastp_command ‑‑fastp_options_string ‑‑min_paired_end_reads_overlap ‑‑max_paired_end_reads_overlap ‑‑stringent_flash_merging ‑‑quantification_window_size ‑‑quantification_window_center ‑‑exclude_bp_from_left ‑‑exclude_bp_from_right ‑‑use_legacy_insertion_quantification ‑‑ignore_substitutions ‑‑ignore_insertions ‑‑ignore_deletions ‑‑discard_indel_reads ‑‑needleman_wunsch_gap_open ‑‑needleman_wunsch_gap_extend ‑‑needleman_wunsch_gap_incentive ‑‑needleman_wunsch_aln_matrix_loc ‑‑plot_histogram_outliers ‑‑plot_window_size ‑‑min_frequency_alleles_around_cut_to_plot ‑‑expand_allele_plots_by_quantification ‑‑allele_plot_pcts_only_for_assigned_reference ‑‑quantification_window_coordinates ‑‑annotate_wildtype_allele ‑‑keep_intermediate ‑‑dump ‑‑write_detailed_allele_table ‑‑fastq_output ‑‑bam_output ‑‑bowtie2_index ‑‑zip_output ‑‑max_rows_alleles_around_cut_to_plot ‑‑suppress_report ‑‑place_report_in_output_folder ‑‑suppress_plots ‑‑base_editor_output ‑‑conversion_nuc_from ‑‑conversion_nuc_to ‑‑prime_editing_pegRNA_spacer_seq ‑‑prime_editing_pegRNA_extension_seq ‑‑prime_editing_pegRNA_extension_quantification_window_size ‑‑prime_editing_pegRNA_scaffold_seq ‑‑prime_editing_pegRNA_scaffold_min_match_length ‑‑prime_editing_nicking_guide_seq ‑‑prime_editing_override_prime_edited_ref_seq ‑‑prime_editing_override_sequence_checks ‑‑crispresso1_mode ‑‑dsODN ‑‑auto ‑‑debug ‑‑no_rerun ‑‑n_processes ‑‑bam_input ‑‑bam_chr_loc ‑‑batch_settings ‑‑skip_failed ‑‑min_reads_for_inclusion ‑‑batch_output_folder ‑‑suppress_batch_summary_plots ‑‑crispresso_command ‑‑disable_guardrails ‑‑use_matplotlib ‑‑halt_on_plot_fail