![]() These differences entailed disparate results, which were further sensitive to processing settings leading to different biological interpretations in the worst case. While it was possible to construct RNA-seq analysis WFs with all three WFMS tools, the constructed WFs are different. Results: Since we already decided on the three WMFS, many of the criteria we suggest for WFMS evaluation do not apply to our situation and we focus on the WF creation here. KNIME lags behind in these two aspects but excels at other levels, such as machine learning. In summary, Galaxy currently provides the most significant number of analysis tools for RNA-seq, while CLC offers the most intuitive visualization. Four different workflows (WFs) performing RNA-seq data analysis were successfully constructed in all three WFMS. Methods: These tools were compared using a variety of criteria ranging from installation to workflow execution and sharing. In this work, we created RNA-seq data analysis workflows in three WFMS, namely Galaxy (free, open-source), KNIME (free, commercial, and partially open source), and CLC (commercial, closed source). However, the use of workflow management systems (WFMS) should be encouraged in order to enhance result reproducibility, to establish best data analysis practices, and to share such data analysis workflows. Often ad hoc scripts are used for such analyses. Raw RNA-seq data passes through a multi-step computational pipeline to derive meaning from such measurements. RNA sequencing (RNA-seq) allows qualitative and quantitative RNA expression analysis. We can chat about your project and make recommendations to get you the help you need to proceed.Background: Transcriptional changes are hallmarks of development and disease. Not sure where to start? Just stop by NRB 933C. We have experience using Cell Profiler and Image analysis, as well as connections to many of the image analysis core facilities on campus. In addition, we can follow the R introductory course with advice tailored to your project, in consultations that can range from brief visits to yearlong support. We provide guidance on how to configure and use R, the main workhorse of immunogenomics, and how to develop project-specific analysis paths with RStudio. We have experience with clinical trial experimental design, differential expression analysis, as well as general statistics. General statistics advice and consulting services are available for help with experimental design or how to compare results from expression analysis. Seurat: We provide general consulting help on how to use Seurat We can help facilitate advice gathering from experts in the area.Ĭell Ranger: We have a Cell Ranger pipeline for department members This includes but is not limited to the Single Cell Genomics Core at BWH, as well as the Single Cell Core at HMS. In addition, we have connections to single cell cores in the Longwood Medical Area. We provide advice and training support for both Cell Ranger and Seurat. We have a robust workflow and tutorial along with experts to help you through this process. The second option involves using CLC Genomics workbench ( Link) this is software package is installed on several of the machines in the IT suite (NRB933). For this option there are several ready built pipelines available for researchers to use. There are two major solutions that we have available: The first option involves using to the schools' computing cluster (O2) this would involve using software such as the Tuxedo Suite ( Link). We provide a number of solutions for analyzing RNA-seq data, and we are here to help provide guidance throughout this process. ![]()
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