CRISPRseq Report — nf-core/CRISPRseq

1. Project Overview

Total Samples

processed

Total Input Reads

8.07M

across all samples

Median Read Length

424

Avg Aligned Reads

81.24%

of raw reads

Avg WT (PF)

89.04%

passing filter

Study design: Edit detection using gRNA and the provided template sequence. The analysis quantifies editing outcomes and quality-control metrics for each sample.

2. Methods

Processing follows the nf-core/CRISPRseq workflow. Reads are QC-checked, adapter-trimmed, merged, and filtered prior to alignment. Editing outcomes are quantified across indels and substitutions, with classification into WT versus edited reads and frame-aware indel categories.

3. Summary Tables

Alignment Summary (Percent of Raw Reads)

Sample	raw-reads	Merged %	Reads w/ Adapters %	Quality Filtered %	UMI Clustered %	Aligned %
Sample6	1,228,012	83.90%	83.73%	83.51%	83.51%	82.82%
Sample8	1,197,007	77.12%	76.89%	76.96%	76.96%	76.19%
Sample7	1,305,159	56.33%	56.18%	55.73%	55.73%	55.23%
Sample5	1,301,542	89.38%	89.21%	89.30%	89.30%	88.70%
Sample4	1,433,009	56.43%	56.29%	56.32%	56.32%	55.80%
Sample1	1,124,113	97.16%	96.73%	97.09%	97.09%	96.84%
Sample2	1,298,139	97.73%	97.37%	97.67%	97.67%	97.49%
Sample3	1,094,404	97.18%	96.78%	97.10%	97.10%	96.85%

Edit Summary (Percent of Passing Filter Reads)

Sample	Total (Passing Filter)	WT %	Delins %	Ins In-frame %	Ins Out-of-frame %	Dels In-frame %	Dels Out-of-frame %
Sample1	1,083,440	97.71%	0.02%	0.01%	0.49%	0.02%	1.75%
Sample2	1,259,379	97.67%	0.02%	0.01%	0.49%	0.02%	1.79%
Sample3	1,048,898	73.11%	0.02%	0.01%	0.37%	0.02%	26.47%
Sample4	745,077	91.95%	0.10%	0.00%	0.41%	3.41%	4.13%
Sample5	1,112,675	95.34%	0.12%	0.00%	0.47%	1.90%	2.17%
Sample6	1,006,708	98.94%	0.11%	0.00%	0.48%	0.03%	0.44%
Sample7	700,926	96.52%	0.10%	0.00%	0.45%	1.26%	1.66%
Sample8	687,382	61.11%	0.79%	0.00%	0.29%	19.08%	18.73%

4. Results

Figures 1–6 are presented in numerical order and labeled with the sample ID used for each panel.

Sample2 deletions — **Figure 1.** Highlights the most frequent deletion alleles. The x-axis marks genomic positions; the y-axis shows each deletion’s share among all deletions, with the deletion length annotated. Dashes indicate removed bases.
*Sample: Sample2*

Figure 2. Shows base composition within ±25 bp of the cut site. Each bar reports the dominant nucleotide and its percentage; the protospacer bases are labeled on the axis. Positions exceeding 90% are left uncolored.
Sample: Sample2

Figure 3. Proportion of the most frequent edits with WT included; each label denotes position, edit type, length, and sequence.
Sample: Sample8

Figure 4. Distribution of edit classes: WT versus indels, with indels partitioned into deletions, insertions, and delins and stratified by frame.
Sample: Sample8

Figure 5. Read progression through processing steps from raw input to UMI-clustered reads.
Sample: Sample8

Figure 6. QC classification of aligned reads into WT and indel categories with filtering and edit-window criteria.
Sample: Sample8

6. References

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276–278. doi:10.1038/s41587-020-0439-x
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316–319. doi:10.1038/nbt.3820
Sanvicente-García M, García-Valiente A, Jouide S, Jaraba-Wallace J, Bautista E, Escobosa M, et al. CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing. PLoS Comput Biol. 2023;19(5):e1011137. doi:10.1371/journal.pcbi.1011137
Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048. doi:10.1093/bioinformatics/btw354
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–3100. doi:10.1093/bioinformatics/bty191
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Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079. doi:10.1093/bioinformatics/btp352
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FastQC. Babraham Bioinformatics. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
PEAR (Paired-End reAd mergeR). Available from: https://cme.h-its.org/exelixis/web/software/pear/
Seqtk. Available from: https://github.com/lh3/seqtk
Docker. Merkel D. Docker: lightweight Linux containers for consistent development and deployment. Linux J. 2014;2014(239).

CRISPRseq Analysis Report