Which module is used for count matrix after trinity output
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: https://github.com/trinityrnaseq/trinityrnaseq/wiki
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: https://galaxyproject.org/use/
Trinity CTAT Galaxy Author’s server with their version of the wrapped tools.
Galaxy Europe Alternative server that also includes the latest IUC wrapped “Trinity tool suite” tools
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: https://github.com/galaxyproject/training-material/pull/1351