Hello, I have a question about DESeq2 with pair end file.
I generated StringTie on collection from pair end, RNA-seq raw data.
However, I can’t put on each file for factor level of DESeq2.
How can I solve this?
Tutorials from Transcriptomics workflows can be found here, and cover your use case (probably…) → Galaxy Training!
Some simple “rules” about using these tools have an FAQ that is worth reviewing, too. See → Extended Help for Differential Expression Analysis Tools
Are all of the samples in a single dataset collection? If so, you might need to use one collection per sample (all replicates for a single sample can be together) or if you are using group tags and a workflow, all of the samples can be together in the same collection, along with a matrix that tells the tool which samples belong to which factor group.
Examples for all of the above are in the tutorials and in the help section for the DESeq2 tool.
If you need more help, please share more details. A shared history along with a few screenshots seem appropriate. This FAQ lists out the kind of information to post back so others can help you → Troubleshooting errors.
But, do review the tutorials – I think you will find what is going wrong faster that way, and with more details than we can reproduce here. And, you can use those tutorial examples to explain what is going wrong with your analysis. 
Each of those tutorials also include a workflow that can be imported and customized. Much faster than trying to click around for every step, every sample, and less error prone.