biostudies-literatureUnknownMills WTBraude Foundation awardNIMH NIH HHSMaryland Stem Cell Research Fund Launch ProgramNational Institutes of HealthBlaustein Endowment for Pain Research and EducationMicroRNAs (miRNAs) are small non-coding RNAs (sncRNAs) that function in post-transcriptional gene regulation through imperfect base pairing with mRNA targets which results in inhibition of translation and typically destabilization of bound transcripts. Sequence-based algorithms historically used to predict miRNA targets face inherent challenges in reliably reflecting in vivo interactions. Recent strategies have directly profiled miRNA-target interactions by crosslinking and ligation of sncRNAs to their targets within the RNA-induced silencing complex (RISC), followed by high throughput sequencing of the chimeric sncRNA:target RNAs. Despite the strength of these direct profiling approaches, standardized pipelines for effectively analyzing the resulting chimeric sncRNA:target RNA sequencing RNA (New York, N.Y.)rna.079240.122https://www.ebi.ac.uk/biostudies/studies/S-EPMC9808574biostudies-literatureSCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data.PMC9808574F31 MH124282F31MH124282Meffert MKEadara SJaffe AEMills WTfalseSCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data.MicroRNAs (miRNAs) are small non-coding RNAs (sncRNAs) that function in post-transcriptional gene regulation through imperfect base pairing with mRNA targets which results in inhibition of translation and typically destabilization of bound transcripts. Sequence-based algorithms historically used to predict miRNA targets face inherent challenges in reliably reflecting in vivo interactions. Recent strategies have directly profiled miRNA-target interactions by crosslinking and ligation of sncRNAs to their targets within the RNA-induced silencing complex (RISC), followed by high throughput sequencing of the chimeric sncRNA:target RNAs. Despite the strength of these direct profiling approaches, standardized pipelines for effectively analyzing the resulting chimeric sncRNA:target RNA sequencing 2022-01-01T00:00:00Z2022 Oct2026-05-28T02:14:30.753Z2025-04-26T20:29:10.637ZS-EPMC98085743631608610.1261/rna.079240.122