Resolves conflicts due to repeated sequences in RNA. Barnacle is a pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo transcriptome assembly. It identifies sequences with a variety of anomalous alignment topologies, predicts partial tandem duplications (PTDs), internal tandem duplications (ITDS), and fusions from these sequences, and measures the coverage of the inferred chimeric transcripts relative to corresponding wild-type transcripts.
Recognizes chimeras corresponding to potential L1 Chimeric Transcripts (LCTs) in RNA-seq data from one or several samples. CLIFinder aims to analyze stranded paired-end RNA-seq data. It can be useful for genome-wide analyses of LCT expression in different tissues, in normal or pathological conditions. This tool is customizable and can be adapted for investigation of transcription from other repeat types.
Identifies non-coding RNA (ncRNA) ends with terminal stem-loops by using chimeric reads from RNA-seq data. Vicinal exploits the self-priming and ligation property of ncRNA 3’ and 5’ terminal stem-loops during library preparation via the Gubler-Hoffman method and massively parallel sequencing. This software maps the unmapped fragments to the vicinity of the mapped fragments.