Genes to transcript file for building expression matrix/ DEseq2/ edgeR differential expression

usegalaxy.org support
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Hello @Satya_Mitra

It sounds like you are still using the older version of Trinity. A new version is available. Trinity itself will now output a genes-to-transcript mapping.

I added more details to a prior post about this same topic. Please review. If you are mixing the older Trinity output with the newer tools included in the updated tool suite, unexpected issues may come up. It would be better to use all of the updated tools to avoid technical problems (errors) or scientific problems (content) – and the latter may be difficult to detect.

Start there, then come back and ask another question if you are still stuck.

Do keep in mind that very large unfiltered assembly datasets may not process well at public servers due to exceeding resources (or you may run into other limits, like the web-Blat query at UCSC). But there are methods to reduce the data in meaningful ways. Review the Trinity suites tool forms – each explains the expected inputs and which tools produce them, and those all correspond to the original Trinity tool author’s workflow guidance (linked into each tool form in the help section).

If your work is actually too large to run at public Galaxy servers, you can set up your own Galaxy and allocate sufficient resources. There are a few ways to do this. Start with the resources below if this option interests you.

Thanks!