Hi @luweidong and @Sutrisha_Kundu
Everyone could use rnaSPAdes instead!
We are getting ready to deprecate all Trinity tools at UseGalaxy.org due to age and inefficiency in how the tools work. Note that the Trinity tools will still be available, but will not be supported after today.
Also, only one Trinity assembly will run at a time at UseGalaxy.org, so plan for those delays. rnaSPAdes will run as usual with concurrent job processing.. How other public servers run these tools is not part of this particular resource adjustment.
Galaxy Training Network
https://training.galaxyproject.org ← search with the keyword “quality” to find help for QA. Assembly is very sensitive to read quality and should never be skipped.
Transcriptomics / Tutorial List ← see the Intro tutorials here, and the end-to-end trio, for alternatives if the goal is to do RNA-seq DE analysis. Actual assembly is not needed unless you plan to do variant calling or something similar…
FAQ: Extended Help for Differential Expression Analysis Tools ← tips for preparing your reference data
Galaxy Help forum
https://help.galaxyproject.org << legacy troubleshooting help is here about this tool, so try a search with the tool name
Running pooled samples is unlikely to work well at UseGalaxy.org. If this is what you really need to do, try at UseGalaxy.eu since they can scale up the largest for this tool. Plan for the time needed to queue and execute, and let the jobs complete. Or, you could explore private options like AnVIL - Galaxy Community Hub