Reference-based RNA-Seq data analysis

I am doing Reference-based RNA-Seq data analysis but in the DESeq2 part in “Select groups that correspond to this factor level” it says that “no options available”. How can I solve this problem?

Welcome, @aysu

In general, when a tool form does not recognize an input, one of these is going on:

  1. The dataset’s datatype is not a match for the expected the inputs
  2. That data is in a collection, so the input option needs to be toggled to the folder icon. That collection needs to include datasets with the proper datatype.
  3. Or, maybe those files have not been produced?
  4. Or, are in a different history? Tools can only “see” what is in the active history. You can switch histories using the double-arrow icon or under User → Histories.

If you are following the tutorial exactly, the data are referenced by tags assigned to collections, so if you didn’t do that part yet, it will be needed now. If you did add tags, maybe that didn’t work as expected? You can inspect those elements under the history “hidden” tab, or click into the collection.


  1. Determining what datatype(s) any tool is expecting (not just fastq): fastq unavailable -- Tool does not recognize inputs? How to check why - #2 by jennaj
  2. Collections &&


If you need more help, maybe a screenshot would help to explain what you are seeing? Try to capture the full screen, including the server URL, and expand the datasets in the history you think should be selected. Troubleshooting errors && What information should I include when reporting a problem?