{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["14(5)"],"submitter":["Wang Y"],"pubmed_abstract":["RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Current obstacles in analyzing RNA-seq data include a lack of functional annotation, which may complicate the process of linking genes to corresponding functions. Here, we provide a one-stop RNA-seq analysis pipeline, PipeOne-NM, for transcriptome functional annotation, non-coding RNA identification, and transcripts alternative splicing analysis of non-model organisms, intended for use with Illumina platform-based RNA-seq data. We performed PipeOne-NM on 237 <i>Schmidtea mediterranea</i> RNA-seq run"],"journal":["Genes"],"pagination":["989"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10218480"],"repository":["biostudies-literature"],"pubmed_title":["Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in <i>Schmidtea mediterranea</i>."],"pmcid":["PMC10218480"],"pubmed_authors":["Xiong Y","Songyang Z","Li S","Nong B","Xu S","Zhou W","Wang Y"],"additional_accession":[]},"is_claimable":false,"name":"Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in <i>Schmidtea mediterranea</i>.","description":"RNA sequencing (RNA-seq) is a high-throughput technology that provides in-depth information on transcriptome. The advancement and dropping costs of RNA sequencing, accompanied by more available reference genomes for different species, make transcriptome analysis in non-model organisms possible. Current obstacles in analyzing RNA-seq data include a lack of functional annotation, which may complicate the process of linking genes to corresponding functions. Here, we provide a one-stop RNA-seq analysis pipeline, PipeOne-NM, for transcriptome functional annotation, non-coding RNA identification, and transcripts alternative splicing analysis of non-model organisms, intended for use with Illumina platform-based RNA-seq data. We performed PipeOne-NM on 237 <i>Schmidtea mediterranea</i> RNA-seq run","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Apr","modification":"2025-04-05T14:15:34.353Z","creation":"2025-04-05T14:15:34.353Z"},"accession":"S-EPMC10218480","cross_references":{"pubmed":["37239350"],"doi":["10.3390/genes14050989"]}}