Hello, I am very new to this, so forgive me if I’m missing something but I’ve come across massive discrepancies between processing the same files on the same supposed tools on the EU vs Org sites. The first issue I had was when trying to map paired fastq files on the EU site using “Map with BWA-MEM…

Hi @M.r.t Thanks for sharing the histories! Very helpful. It looks like the reads from the pair didn’t load completely from the SRA at the UseGalaxy.eu server. This then lead to the downstream result discrepancy when mapping. Some mapping tools may have trapped this but I wouldn’t count on that – …

Hi @M.r.t Sorry to hear that you have been having problems. The tools across servers should be exact. Maybe we can discover what the differences are so you can get the results synced up? Using a workflow would be one way to do this since all of the details would be in the workflow: tool versions, …

Hi @jennaj . A chat message will be better. I’m not sure how to send one here

I just sent you a message to get it started. I included instructions for how to share in there too. Find your messages at the very top right at this site, under your account icon. [Screen Shot 2025-04-21 at 1.05.48 PM]

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Large discrepancies between processing identical files on Org vs EU site

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