Hi,
I am new to Galaxy and I am analyzing publicly available RNA-seq data from GEO (accession: GSE233242).
Steps I performed:
Uploaded paired-end FASTQ files to Galaxy Europe (usegalaxy.eu)
Ran FastQC successfully on both files
Then ran Trimmomatic in paired-end mode
However, all Trimmomatic output datasets failed (R1 paired, R2 paired, and both unpaired outputs are red in the history). No trimmed files were produced.
Details:
Data type: Paired-end RNA-seq
Input format: fastq.gz
FastQC completed without errors
Error message from Galaxy job details:
PASTE THE FULL ERROR MESSAGE FROM THE JOB STDERR HERE
I am not sure whether the issue is related to file pairing, FASTQ format, or Trimmomatic parameters. Any help would be greatly appreciated.
Thank you.
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Mahsa80.mm •
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Galaxy has a dedicated user support forum; post the issue there as well. https://help.galaxyproject.org/c/usegalaxy-eu-support/6
show the command that has been run,
if you get no results, typically it means that one of the settings filtered out all reads, for example all resulting readlenghts are under the cutoff