Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts
Dual RNA-Seq technology has significantly advanced the study of biological interactions between two organisms by allowing parallel transcriptomic analysis. Existing analysis methods employ various combinations of open-source bioinformatics tools to process dual RNA-Seq data. Upon reviewing these met...
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Bio-protocol LLC
2025-02-01
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| author | Infanta Eden M. Umashankar Vetrivel |
| author_facet | Infanta Eden M. Umashankar Vetrivel |
| author_sort | Infanta Eden M. |
| collection | DOAJ |
| description | Dual RNA-Seq technology has significantly advanced the study of biological interactions between two organisms by allowing parallel transcriptomic analysis. Existing analysis methods employ various combinations of open-source bioinformatics tools to process dual RNA-Seq data. Upon reviewing these methods, we intend to explore crucial criteria for selecting standard tools and methods, especially focusing on critical steps such as trimming and mapping reads to the reference genome. In order to validate the different combinatorial approaches, we performed benchmarking using top-ranking tools and a publicly available dual RNA-Seq Sequence Read Archive (SRA) dataset. An important observation while evaluating the mapping approach is that when the adapter trimmed reads are first mapped to the pathogen genome, more reads align to the pathogen genome than the unmapped reads derived from the traditional host-first mapping approach. This mapping method prevents the misalignment of pathogen reads to the host genome due to their shorter length. In this way, the pathogenic read information found at lesser proportions in a complex eukaryotic dataset is precisely obtained. This protocol presents a comprehensive comparison of these possible approaches, resulting in a robust unified standard methodology. |
| format | Article |
| id | doaj-art-9072d6f379ea445b94b23fa2d4ebb9b4 |
| institution | Kabale University |
| issn | 2331-8325 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Bio-protocol LLC |
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| series | Bio-Protocol |
| spelling | doaj-art-9072d6f379ea445b94b23fa2d4ebb9b42025-02-07T08:16:46ZengBio-protocol LLCBio-Protocol2331-83252025-02-0115310.21769/BioProtoc.5182Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic HostsInfanta Eden M.0Umashankar Vetrivel1Department of Virology and Biotechnology, Bioinformatics Division, Indian Council for Medical Research-National Institute for Research in Tuberculosis (ICMR-NIRT), Chennai, IndiaDepartment of Virology and Biotechnology, Bioinformatics Division, Indian Council for Medical Research-National Institute for Research in Tuberculosis (ICMR-NIRT), Chennai, IndiaDual RNA-Seq technology has significantly advanced the study of biological interactions between two organisms by allowing parallel transcriptomic analysis. Existing analysis methods employ various combinations of open-source bioinformatics tools to process dual RNA-Seq data. Upon reviewing these methods, we intend to explore crucial criteria for selecting standard tools and methods, especially focusing on critical steps such as trimming and mapping reads to the reference genome. In order to validate the different combinatorial approaches, we performed benchmarking using top-ranking tools and a publicly available dual RNA-Seq Sequence Read Archive (SRA) dataset. An important observation while evaluating the mapping approach is that when the adapter trimmed reads are first mapped to the pathogen genome, more reads align to the pathogen genome than the unmapped reads derived from the traditional host-first mapping approach. This mapping method prevents the misalignment of pathogen reads to the host genome due to their shorter length. In this way, the pathogenic read information found at lesser proportions in a complex eukaryotic dataset is precisely obtained. This protocol presents a comprehensive comparison of these possible approaches, resulting in a robust unified standard methodology.https://bio-protocol.org/en/bpdetail?id=5182&type=0 |
| spellingShingle | Infanta Eden M. Umashankar Vetrivel Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts Bio-Protocol |
| title | Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts |
| title_full | Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts |
| title_fullStr | Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts |
| title_full_unstemmed | Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts |
| title_short | Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts |
| title_sort | optimal dual rna seq mapping for accurate pathogen detection in complex eukaryotic hosts |
| url | https://bio-protocol.org/en/bpdetail?id=5182&type=0 |
| work_keys_str_mv | AT infantaedenm optimaldualrnaseqmappingforaccuratepathogendetectionincomplexeukaryotichosts AT umashankarvetrivel optimaldualrnaseqmappingforaccuratepathogendetectionincomplexeukaryotichosts |