GSE152684

Discovery and evaluation of CRISPR/Cas-mediated systems for site-specific RNA editing

1. Raw reads were adapter-trimmed using Cutadapt (version 1.14)
2. Sequenced reads were aligned to hg19 genome using STAR (version 2.5.2b) and sorted using samtools (version 1.5)
3. Gene counts were quantified from sorted BAM files using featureCounts (version 1.5.0) of the Subread (Liao et al., Nucleic Acids Research 2013) package using "gene" as a metafeature.
4. Annotated gene length and gene counts were subsequently used to calculate transcript per-million (TPM) for each gene in each library.
5. For downsampling prior to downstream editing analysis, samtools view -bs INT.FRAC was used for proportional downsampling of read pairs to achieve sampling depth between 15-35 million aligned reads
6. Aligned BAM files were run through SAILOR (v1.0.4) using the following parameters-- min_variant_coverage: 5, alpha: 0, beta: 0, edit_fraction: 0.01
7. BED files that are output corresponding to positive and negative strands of the genome from SAILOR are combined into one BED file and filtered based upon confidence score (Washburn et al., Cell Reports 2014)
8. Recurrent sites between replicates were determined using pybedtools (version 0.8.0) intersect with the following options: wo=True, s=True

Supplementary Files (3)

Dataset Citations (1)

Linked Publications (1)