Overview

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File Description Type
CRISPRessoBatch_on_crispresso_batch.html CRISPResso report result

Sample list
Sample OriginalID
Sample001 Sample001
Sample002 Sample002
Sample003 Sample003
Sample004 Sample004
Sample005 Sample005
Sample006 Sample006
Sample007 Sample007
Sample008 Sample008
Sample009 Sample009
Sample010 Sample010

Method: cutadaptMartin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1):10-12. doi:https://doi.org/10.14806/ej.17.1.200 (version: 4.4)

Sequencing trimming using cutadapt

Custom Parameters
  • -a = AGACCAAGTCTCTGCTACCGTA
  • -A = TGTAGAACCATGTCGTCAGTGT
  • --report = minimal
  • -m = 50
Method: Quality trimming

Quality trimming based on quality threshold and length parameters.

Custom Parameters
  • min length = 50
Method: Adapter trimming

Adapter/primer sequences were trimmed from the reads.

Custom Parameters
  • 5' adapter = AGACCAAGTCTCTGCTACCGTA
  • 5' adapter (read2) = TGTAGAACCATGTCGTCAGTGT

Figure 1 . Trimming results

Table 1 . Trimming statistics

Table 1 . Trimming statistics
Sample Trim passed Ambig dropped Trim filter dropped Trim length dropped Percent passed Mean Length Mean Trimmed Length Quality trimmed bp
Sample001 14881 0 0 10 99.93% 306.0 305.6 0
Sample002 12102 0 0 5 99.96% 306.0 305.6 0
Sample003 10792 0 0 21 99.81% 306.0 305.6 0
Sample004 12120 0 0 7 99.94% 306.0 305.7 0
Sample005 12452 0 0 9 99.93% 306.0 305.0 0
Sample006 12317 0 0 9 99.93% 306.0 305.1 0
Sample007 9308 0 0 13 99.86% 306.0 305.9 0
Sample008 7667 0 0 28 99.64% 306.0 305.9 0
Sample009 9070 0 0 6 99.93% 306.0 305.9 0
Sample010 6422 0 0 2956 68.48% 306.0 305.2 0

Method: CRISPResso 2Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019 Mar; 37(3):224-226. doi: 10.1038/s41587-019-0032-3. PubMed PMID: 30809026.

Analysis of genome editing outcomes from deep sequencing data

Custom Parameters
  • amplicon_sequence = TAAACTACCAGAAGTATCAGTGCTAAAAGTATCCTTTTCTTTCCTACAGATTCCTCCTTATGGCCAACAAGGCCCCAGCGGGTATGGTCAGCAGGGCCAGACTCCATATTACAACCAGCAAAGTCCTCACCCCCAGCAGCAGCAGCCACCCTACTCTCAGCAACCACCATCCCAGACCCCTCATGCTCAACCTTCATATCAGCAGCAGCCTCAGTCTCAGCCACCACAGCTCCAGTCATCTCAGCCTCCATATTCCCAGCAGCCA
  • sgRNA = GGACTTTGCTGGTTGTAATA

Figure 1 . Overview of mapping statistics

Figure 2 . Overview of quantification

Table 1 . Mapping statistics

Table 1 . Mapping statistics
Sample READS IN INPUTS READS AFTER PREPROCESSING READS ALIGNED N_COMPUTED_ALN N_CACHED_ALN N_COMPUTED_NOTALN N_CACHED_NOTALN
Sample001 14881 14518 14424 1609 12815 29 65
Sample002 12102 11721 11583 3187 8396 62 76
Sample003 10792 10456 10360 2845 7515 42 54
Sample004 12120 11903 11848 1404 10444 13 42
Sample005 12452 12063 11785 3064 8721 105 173
Sample006 12317 11880 11619 3342 8277 100 161
Sample007 9308 9138 9101 1176 7925 15 22
Sample008 7667 7439 7374 886 6488 36 29
Sample009 9070 8830 8789 1154 7635 24 17
Sample010 0 0 0 0 0 0 0

Table 2 . Quantification statistics

Table 2 . Quantification statistics
Sample UNMODIFIED MODIFIED AMBIGUOUS Percent UNMODIFIED Percent MODIFIED Percent AMBIGUOUS
Sample001 14332 92 0 99.4 % 0.638 % 0 %
Sample002 3844 7739 0 33.2 % 66.8 % 0 %
Sample003 3374 6986 0 32.6 % 67.4 % 0 %
Sample004 11784 64 0 99.5 % 0.54 % 0 %
Sample005 4723 7062 0 40.1 % 59.9 % 0 %
Sample006 4411 7208 0 38 % 62 % 0 %
Sample007 50 9051 0 0.549 % 99.5 % 0 %
Sample008 7 7367 0 0.0949 % 99.9 % 0 %
Sample009 1 8788 0 0.0114 % 100 % 0 %

Citations