Converting Transcript Id with Ensemble or Entraz ID ?

usegalaxy.org support
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That Replace tool will transform IDs if you need to. It accepts any two column tabular mapping file. The ID it changes has to be in the first column of your input dataset. There are other ways to do that of course – many tools will match up data based on a common value, that one just happens to do the replace all in one step. Values in other fields are not modified.

The goseq tool does not look up transcriptIDs, but geneIDs. Maybe that is where you are confused? A transcript-to-gene mapping input is required.

Other troubleshooting help that has resolved usage issues in the past for goseq:

  • There should be no versions on transcript or gene names. If present, remove those (the . dot and any number after).
  • A correctly formatted transcript-to-gene reference is needed for the goseq tool. The IDs from all inputs need to match. This input can be a gtf dataset (with no header lines) or a two column tabular dataset. A gff3 annotation will not work. Sorry, wrong advice, this particular tool does not need a mapping file of this type, all inputs are already summarized by geneID (by the tool Featurecounts or however you decide to do the counting).
  • Then confirm that the gene identifier type is match for the chosen “Select Gene ID format”. You could just do a web search with your ID to find out what type it is.
  • Only four genome builds are supported as built-in indexes. Or you can supply one yourself.
  • The format for all the inputs is described in the help section with examples. If any are malformed, the tool will fail.

General FAQ for DE tools. The formatting rules apply not only to DE analysis (are general best practices, summarized, that link to the other FAQs) and covers some of the topics we have discussed when you had trouble with other tools. May help now: Extended Help for Differential Expression Analysis Tools

If you are still stuck after this, are you really working at usegalaxy.org? You could send in a bug report if so. Include a link to this Galaxy help post in the comments and send a reply here, so I know when to look for it. I might recognize what is going wrong. Make sure the error from goseq and all input dataset are left undeleted.

I see several posts from you about this and some are labeled as usegalaxy.eu and some are for usegalaxy.org. Including this one, which does contain a history link: Problem in Goseq tool. Is that still current?