I’m getting different outputs with the same input using the exact same tool of different versions.
I have used Trimmomatic version 0.36.5 on usegalaxy.eu and Trimmomatic version 0.38.0 on usegalaxy.org. I used the same data as inputs. Only difference was the tool versions. And the output I got after trimming from both versions showed different results.
The number of transcripts decreased drastically after trimming with Trimmomatic version 0.38.0 on usegalaxy.org. But the number of transcripts are the same as before trimming with Trimmomatic version 0.36.5 on usegalaxy.eu.
Can anyone please help me understand why I’m getting such different outputs with same toll of different versions?