CRISPResso output

The output of CRISPResso2 consists of a set of informative graphs that allow for the quantification and visualization of the position and type of outcomes within an amplicon sequence.

Data file descriptions

CRISPResso2_report.html is a summary report that can be viewed in a web browser containing all of the output plots and summary statistics.

Alleles_frequency_table.zip can be unzipped to a tab-separated text file that shows all reads and alignments to references. The first column shows the aligned sequence of the sequenced read. The second column shows the aligned sequence of the reference sequence. Gaps in each of these columns represent insertions and deletions. The next column 'Reference_Name' shows the name of the reference that the read aligned to. The fourth column, 'Read_Status' shows whether the read was modified or unmodified. The fifth through seventh columns ('n_deleted', 'n_inserted', 'n_substituted') show the number of bases deleted, inserted, and substituted as compared to the reference sequence. The eighth column shows the number of reads having that sequence, and the ninth column shows the percentage of all reads having that sequence.

CRISPResso_mapping_statistics.txt is a tab-delimited text file showing the number of reads in the input ('READS IN INPUTS') the number of reads after filtering, trimming and merging (READS AFTER PREPROCESSING), the number of reads aligned (READS ALIGNED) and the number of reads for which the alignment had to be computed vs read from cache.

CRISPResso_quantification_of_editing_frequency.txt is a tab-delimited text file showing the number of reads aligning to each reference amplicon, as well as the status (modified/unmodified, number of insertions, deletions, and/or substitutions) of those reads.

CRISPResso_RUNNING_LOG.txt is a text file and shows a log of the CRISPResso run.

CRISPResso2_info.json can be read by other CRISPResso tools and contains information about the run and results.

The remainder of the files are produced for each amplicon, and each file is prefixed by the name of the amplicon if more than one amplicon is given.

Alleles_frequency_table_around_sgRNA_NNNNN.txt is a tab-separated text file that shows alleles and alignments to the specified reference for a subsequence around the sgRNA (here, shown by 'NNNNN'). This data report is produced for each amplicon when a guide is found in the amplicon sequence. A report is generated for each guide. The number of nucleotides shown in this report can be modified by changing the --plot_window_size parameter.

Substitution_frequency_table_around_sgRNA_NNNNN.txt is a tab-separated text file that shows the frequency of substitutions in the amplicon sequence around the sgRNA (here, shown by 'NNNNN'). The first row shows the reference sequence. The following rows show the number of substitutions to each base. For example, the first numeric value in the second row (marked ‘A’) shows the number of bases that have a substitution resulting in an A at the first basepair of the amplicon sequence. The number of unmodified bases at each position is now shown in this table (because they aren’t substitutions). Thus, if the first basepair of the amplicon sequence is an A, the first value in the first row will show 0. A report is generated for each guide. The number of nucleotides shown in this report can be modified by changing the --plot_window_size parameter.

Substitution_frequency_table.txt is a tab-separated text file that shows the frequency of substitutions in the amplicon sequence across the entire amplicon. The first row shows the reference sequence. The following rows show the number of substitutions to each base. For example, the first numeric value in the second row (marked ‘A’) shows the number of bases that have a substitution resulting in an A at the first basepair of the amplicon sequence. The number of unmodified bases at each position is now shown in this table (because they aren’t substitutions). Thus, if the first basepair of the AMPLICON sequence is an A, the first value in the first row will show 0.

Insertion_histogram.txt is a tab-separated text file that shows a histogram of the insertion sizes in the amplicon sequence in the quantification window. Insertions outside of the quantification window are not included. The ins_size column shows the insertion length, and the fq column shows the number of reads having that insertion size.

Deletion_histogram.txt is a tab-separated text file that shows a histogram of the deletion sizes in the amplicon sequence in the quantification window. Deletions outside of the quantification window are not included. The del_size column shows length of the deletion, and the fq column shows the number of reads having that number of substitutions.

Substitution_histogram.txt is a tab-separated text file that shows a histogram of the number of substitutions in the amplicon sequence in the quantification window. Substitutions outside of the quantification window are not included. The sub_count column shows the number of substitutions, and the fq column shows the number of reads having that number of substitutions.

Effect_vector_insertion.txt is a tab-separated text file with a one-row header that shows the percentage of reads with an insertion at each base in the reference sequence. The first column shows the 1-based position of the amplicon, and the second column shows the percentage of reads with a insertion at that location.

Effect_vector_deletion.txt is a tab-separated text file with a one-row header that shows the percentage of reads with a deletion at each base in the reference sequence. The first column shows the 1-based position of the amplicon, and the second column shows the percentage of reads with a deletion at that location.

Effect_vector_substitution.txt is a tab-separated text file with a one-row header that shows the percentage of reads with a substitution at each base in the reference sequence. The first column shows the 1-based position of the amplicon, and the second column shows the percentage of reads with a substitution at that location.

Effect_vector_combined.txt is a tab-separated text file with a one-row header that shows the percentage of reads with any modification (insertion, deletion, or substitution) at each base in the reference sequence. The first column shows the 1-based position of the amplicon, and the second column shows the percentage of reads with a modification at that location.

Modification_count_vectors.txt is a tab-separated file showing the number of modifications for each position in the amplicon. The first row shows the amplicon sequence, and successive rows show the number of reads with insertions (row 2), insertions_left (row 3), deletions (row 4), substitutions (row 5) and the sum of all modifications (row 6). Additionally, the last row shows the number of reads aligned.

If an insertion occurs between bases 5 and 6, the insertions vector will be incremented at bases 5 and 6. However, the insertions_left vector will only be incremented at base 5 so the sum of the insertions_left row represents an accurate count of the number of insertions, whereas the sum of the insertions row will yield twice the number of insertions.

Quantification_window_modification_count_vectors.txt is a tab-separated file showing the number of modifications for positions in the quantification window of the amplicon. The first row shows the amplicon sequence in the quantification window, and successive rows show the number of reads with insertions (row 2), insertions_left (row 3), deletions (row 4), substitutions (row 5) and the sum of all modifications (row 6). Additionally, the last row shows the number of reads aligned.

Nucleotide_frequency_table.txt is a tab-separated file showing the number of each residue at each position in the amplicon. The first row shows the amplicon sequence, and successive rows show the number of reads with an A (row 2), C (row 3), G (row 4), T (row 5), N (row 6), or a deletion (-) (row 7) at each position.

Quantification_window_nucleotide_frequency_table.txt is a tab-separated file showing the number of each residue at positions in the quantification window of the amplicon. The first row shows the amplicon sequence in the quantification window, and successive rows show the number of reads with an A (row 2), C (row 3), G (row 4), T (row 5), N (row 6), or a deletion (-) (row 7) at each position.

Nucleotide_percentage_table.txt is a tab-separated file showing the percentage of each residue at each position in the amplicon. The first row shows the amplicon sequence, and successive rows show the percentage of reads with an A (row 2), C (row 3), G (row 4), T (row 5), N (row 6), or a deletion (-) (row 7) at each position.

Quantification_window_nucleotide_percentage_table.txt is a tab-separated file showing the percentage of each residue at positions in the quantification window of the amplicon. The first row shows the amplicon sequence in the quantification window, and successive rows show the percentage of reads with an A (row 2), C (row 3), G (row 4), T (row 5), N (row 6), or a deletion (-) (row 7) at each position.

The following report files are produced when the base editor mode is enabled:

Selected_nucleotide_percentage_table_around_sgRNA_NNNNN.txt is a tab-separated text file that shows the percentage of each base at selected nucleotides in the amplicon sequence around the sgRNA (here, shown by 'NNNNN'). If the base editing experiment targets cytosines (as set by the --base_editor_from parameter), each C in the quantification window will be numbered (e.g. C5 represents the cytosine at the 5th position in the selected nucleotides). The percentage of each base at these selected target cytosines is reported, with the first row showing the numbered cytosines, and the remainder of the rows showing the percentage of each nucleotide present at these locations. This file shows nucleotides within '--plot_window_size' bp of the position specified by the parameter '--quantification_window_center' relative to the 3' end of each guide.

Selected_nucleotide_frequency_table_around_sgRNA_NNNNN.txt is a tab-separated text file that shows the frequency of each base at selected nucleotides in the amplicon sequence around the sgRNA (here, shown by 'NNNNN'). If the base editing experiment targets cytosines (as set by the --base_editor_from parameter), each C in the quantification window will be numbered (e.g. C5 represents the cytosine at the 5th position in the selected nucleotides). The frequency of each base at these selected target cytosines is reported, with the first row showing the numbered cytosines, and the remainder of the rows showing the frequency of each nucleotide present at these locations. This file shows nucleotides within '--plot_window_size' bp of the position specified by the parameter '--quantification_window_center' relative to the 3' end of each guide.

The following report files are produced when the amplicon contains a coding sequence:

Frameshift_analysis.txt is a text file describing the number of noncoding, in-frame, and frameshift mutations. This report file is produced when the amplicon contains a coding sequence.

Splice_sites_analysis.txt is a text file describing the number of splicing sites that are unmodified and modified. This file report is produced when the amplicon contains a coding sequence.

Effect_vector_insertion_noncoding.txt is a tab-separated text file with a one-row header that shows the percentage of reads with a noncoding insertion at each base in the reference sequence. The first column shows the 1-based position of the amplicon, and the second column shows the percentage of reads with a noncoding insertion at that location. This report file is produced when amplicon contains a coding sequence.

Effect_vector_deletion_noncoding.txt is a tab-separated text file with a one-row header that shows the percentage of reads with a noncoding deletion at each base in the reference sequence. The first column shows the 1-based position of the amplicon, and the second column shows the percentage of reads with a noncoding deletion at that location. This report file is produced when amplicon contains a coding sequence.

Effect_vector_substitution_noncoding.txt is a tab-separated text file with a one-row header that shows the percentage of reads with a noncoding substitution at each base in the reference sequence. The first column shows the 1-based position of the amplicon, and the second column shows the percentage of reads with a noncoding substitution at that location. This report file is produced when amplicon contains a coding sequence.