Which module is used for count matrix after trinity output
Welcome @Priya_GNDU!
Tool: Build expression matrix for a de novo assembly of RNA-Seq data by Trinity
Resources for generating/working with Trinity assemblies:
- Author’s Wiki, includes links to tutorials/resources: Home · trinityrnaseq/trinityrnaseq Wiki · GitHub
The Trinity command-line tools are wrapped for Galaxy. Help is on each tool explaining the inputs (and how to create them/tools) plus a description of the output for that step. There are two primary suites/versions, plus other community contributions of wrapped Trinity tools. Search in the ToolShed with the keyword “trinity” to find all.
Good public Galaxy server choices: Galaxy Platform Directory: Servers, Clouds, and Deployable Resources - Galaxy Community Hub
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Trinity CTAT Galaxy Author’s server with their version of the wrapped tools.
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Galaxy Europe Alternative server that also includes the latest IUC wrapped “Trinity tool suite” tools
- Server: https://usegalaxy.eu/
- Directory: UseGalaxy.eu - Galaxy Community Hub
There isn’t a Galaxy Training Network (GTN) tutorial that covers this protocol using the IUC tool versions yet, as far as I know. I asked at the GTN Gitter chat for clarification. Something may be in progress already but not published. They may answer here or there: https://gitter.im/Galaxy-Training-Network/Lobby?at=5dd6ca59afacdc4de44df858 Update: The tutorial is in progress, see: De novo transcriptome assembly, annotation, and differential expression analysis by abretaud · Pull Request #1351 · galaxyproject/training-material · GitHub