CAMPAREE: a robust and configurable RNA expression simulator
Abstract Background The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accurately assess the performance of RNA-Seq analysis methods. However, exist...
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| Format: | Article |
| Language: | English |
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BMC
2021-09-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07934-2 |
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| author | Nicholas F. Lahens Thomas G. Brooks Dimitra Sarantopoulou Soumyashant Nayak Cris Lawrence Antonijo Mrčela Anand Srinivasan Jonathan Schug John B. Hogenesch Yoseph Barash Gregory R. Grant |
| author_facet | Nicholas F. Lahens Thomas G. Brooks Dimitra Sarantopoulou Soumyashant Nayak Cris Lawrence Antonijo Mrčela Anand Srinivasan Jonathan Schug John B. Hogenesch Yoseph Barash Gregory R. Grant |
| author_sort | Nicholas F. Lahens |
| collection | DOAJ |
| description | Abstract Background The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accurately assess the performance of RNA-Seq analysis methods. However, existing RNA-Seq simulators focus on modeling the technical biases and artifacts of sequencing, rather than on simulating the original RNA samples. A first step in simulating RNA-Seq is to simulate RNA. Results To fill this need, we developed the Configurable And Modular Program Allowing RNA Expression Emulation (CAMPAREE), a simulator using empirical data to simulate diploid RNA samples at the level of individual molecules. We demonstrated CAMPAREE’s use for generating idealized coverage plots from real data, and for adding the ability to generate allele-specific data to existing RNA-Seq simulators that do not natively support this feature. Conclusions Separating input sample modeling from library preparation/sequencing offers added flexibility for both users and developers to mix-and-match different sample and sequencing simulators to suit their specific needs. Furthermore, the ability to maintain sample and sequencing simulators independently provides greater agility to incorporate new biological findings about transcriptomics and new developments in sequencing technologies. Additionally, by simulating at the level of individual molecules, CAMPAREE has the potential to model molecules transcribed from the same genes as a heterogeneous population of transcripts with different states of degradation and processing (splicing, editing, etc.). CAMPAREE was developed in Python, is open source, and freely available at https://github.com/itmat/CAMPAREE . |
| first_indexed | 2024-12-14T18:42:52Z |
| format | Article |
| id | doaj.art-e652ef326a1f48d3a154408788505a58 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T18:42:52Z |
| publishDate | 2021-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e652ef326a1f48d3a154408788505a582022-12-21T22:51:27ZengBMCBMC Genomics1471-21642021-09-0122111210.1186/s12864-021-07934-2CAMPAREE: a robust and configurable RNA expression simulatorNicholas F. Lahens0Thomas G. Brooks1Dimitra Sarantopoulou2Soumyashant Nayak3Cris Lawrence4Antonijo Mrčela5Anand Srinivasan6Jonathan Schug7John B. Hogenesch8Yoseph Barash9Gregory R. Grant10The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of PennsylvaniaThe Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of PennsylvaniaThe Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of PennsylvaniaStatistics and Mathematics Unit, Indian Statistical InstituteThe Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of PennsylvaniaThe Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of PennsylvaniaPerelman School of Medicine, Enterprise Research Applications and High Performance Computing, Penn Medicine Academic Computing Services, University of PennsylvaniaThe Institute for Diabetes, Obesity and Metabolism, The Department of Genetics, Perelman School of Medicine, University of PennsylvaniaDivision of Human Genetics, Department of Pediatrics, Center for Chronobiology, Cincinnati Children’s Hospital Medical CenterThe Department of Genetics, Perelman School of Medicine, University of PennsylvaniaThe Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of PennsylvaniaAbstract Background The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accurately assess the performance of RNA-Seq analysis methods. However, existing RNA-Seq simulators focus on modeling the technical biases and artifacts of sequencing, rather than on simulating the original RNA samples. A first step in simulating RNA-Seq is to simulate RNA. Results To fill this need, we developed the Configurable And Modular Program Allowing RNA Expression Emulation (CAMPAREE), a simulator using empirical data to simulate diploid RNA samples at the level of individual molecules. We demonstrated CAMPAREE’s use for generating idealized coverage plots from real data, and for adding the ability to generate allele-specific data to existing RNA-Seq simulators that do not natively support this feature. Conclusions Separating input sample modeling from library preparation/sequencing offers added flexibility for both users and developers to mix-and-match different sample and sequencing simulators to suit their specific needs. Furthermore, the ability to maintain sample and sequencing simulators independently provides greater agility to incorporate new biological findings about transcriptomics and new developments in sequencing technologies. Additionally, by simulating at the level of individual molecules, CAMPAREE has the potential to model molecules transcribed from the same genes as a heterogeneous population of transcripts with different states of degradation and processing (splicing, editing, etc.). CAMPAREE was developed in Python, is open source, and freely available at https://github.com/itmat/CAMPAREE .https://doi.org/10.1186/s12864-021-07934-2SimulationBenchmarkingRNA-Seq |
| spellingShingle | Nicholas F. Lahens Thomas G. Brooks Dimitra Sarantopoulou Soumyashant Nayak Cris Lawrence Antonijo Mrčela Anand Srinivasan Jonathan Schug John B. Hogenesch Yoseph Barash Gregory R. Grant CAMPAREE: a robust and configurable RNA expression simulator BMC Genomics Simulation Benchmarking RNA-Seq |
| title | CAMPAREE: a robust and configurable RNA expression simulator |
| title_full | CAMPAREE: a robust and configurable RNA expression simulator |
| title_fullStr | CAMPAREE: a robust and configurable RNA expression simulator |
| title_full_unstemmed | CAMPAREE: a robust and configurable RNA expression simulator |
| title_short | CAMPAREE: a robust and configurable RNA expression simulator |
| title_sort | camparee a robust and configurable rna expression simulator |
| topic | Simulation Benchmarking RNA-Seq |
| url | https://doi.org/10.1186/s12864-021-07934-2 |
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