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SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data
| Content Provider | Semantic Scholar |
|---|---|
| Author | Yague-Sanz, Carlo Hermand, Damien |
| Copyright Year | 2018 |
| Abstract | Background The spliceosomal transfer of a short spliced leader (SL) RNA to an independent pre-mRNA molecule is called SL trans-splicing and is widespread in the nematode Caenorhabditis elegans. While RNA-sequencing (RNA-seq) data contain information on such events, properly documented methods to extract them are lacking. Findings To address this, we developed SL-quant, a fast and flexible pipeline that adapts to paired-end and single-end RNA-seq data and accurately quantifies SL trans-splicing events. It is designed to work downstream of read mapping and uses the reads left unmapped as primary input. Briefly, the SL sequences are identified with high specificity and are trimmed from the input reads, which are then remapped on the reference genome and quantified at the nucleotide position level (SL trans-splice sites) or at the gene level. Conclusions SL-quant completes within 10 minutes on a basic desktop computer for typical C. elegans RNA-seq datasets and can be applied to other species as well. Validating the method, the SL trans-splice sites identified display the expected consensus sequence, and the results of the gene-level quantification are predictive of the gene position within operons. We also compared SL-quant to a recently published SL-containing read identification strategy that was found to be more sensitive but less specific than SL-quant. Both methods are implemented as a bash script available under the MIT license [1]. Full instructions for its installation, usage, and adaptation to other organisms are provided. |
| Starting Page | 1255 |
| Ending Page | 1256 |
| Page Count | 2 |
| File Format | PDF HTM / HTML |
| PubMed reference number | 30010768v1 |
| Alternate Webpage(s) | https://doi.org/10.1093/gigascience/giy084 |
| DOI | 10.1093/gigascience/giy084 |
| Journal | GigaScience |
| Volume Number | 7 |
| Language | English |
| Access Restriction | Open |
| Subject Keyword | Acclimatization Base Sequence Biopolymer Sequencing Document completion status - Documented Nematodes Nucleotides Operon Pierre Robin Syndrome Quantitation RNA Splicing Reading (activity) Scientific Publication Sequence Number Sleep Polysomnography Domain Trans-Spliced Leader Sequences Trans-Splicing |
| Content Type | Text |
| Resource Type | Article |
