{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR219/065/SRR21958165/SRR21958165.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR219/064/SRR21958164/SRR21958164.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR219/063/SRR21958163/SRR21958163.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR219/066/SRR21958166/SRR21958166.fastq.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Laboratory for functional epigenetics, Department of Human Genetics, KU Leuven"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA891742"],"scientific_name":["Homo sapiens"],"long_description":["Novel single cell RNA-seq analysis combined with CRISPR screens enables the high- throughput characterization of transcriptional changes caused by genetic perturbations. Dedicated software to annotate CRISPR guide RNA (gRNA) libraries and associate them with single cell transcriptomes are however lacking. Here, we generated a CRISPR droplet sequencing dataset. We demonstrate that the current default tool fails to detect mutant gRNAs. We therefore developed GiRAFR, a pysam-based software tool to characterize intact and mutant gRNAs. We show that mutant gRNAs are dysfunctional, and failure to detect and annotate them leads to an inflated estimate of the number of untransformed cells as well as an underestimated multiplet frequency. These findings are mirrored in publicly available datasets, where we find that up to 34 % of cells are transduced with a mutant gRNA. Applying GiRAFR hence stands to improve the annotation and quality of single cell CRISPR screens. Overall design: We transformed A549 cells expressing a tamoxifen-inducible Cas9 with a lentiviral pool for expression of 120 gRNAs at low multiplicity of infection. After stringent selection using puromycin and 2 days of Cas9 induction, cells were allowed to grow for another 5 days."],"tag":["xref:PubMed:37741886"],"repository":["ENA"],"additional_accession":[]},"is_claimable":false,"name":"GiRAFR improves gRNA detection and annotation in single cell CRISPR screens","description":"GiRAFR improves gRNA detection and annotation in single cell CRISPR screens","dates":{"last_updated":"2025-09-24","first_public":"2023-09-30"},"accession":"PRJNA891742","cross_references":{"GEO":["GSE216040"],"taxon":["9606"],"PubMed":["37741886"]}}