Trimmomatic not working on Galaxy.eu


#1

Trimmomatic does not seem to be removing adaptor content in Galaxy.eu.
I submitted the exact same paired-end RNAseq datasets to Galaxy main and Galaxy.eu and ran Trimmomatic with the exact same parameters (Illumina Clip with Truseq3 adaptors for paired end; Sliding Window). Fastqc of trimmed file from Galaxy main looks fine, with adaptor content removed. Fastqc of trimmed file from Galaxy eu looks identical to the fastqc of the raw data i.e. no trimming and clipping of adaptors.
What might be wrong?


#2

Hi Lena,

could you share us your history or the example dataset? Giving you are using the same versions of trimmomatic, this should not happen.

Thanks,
Bjoern


#3

HI Bjoern,

Here is the history in galaxy EU where trimmomatic does not work: https://usegalaxy.eu:/u/lho/h/unnamed-history

Here is the history in galaxy main where trimmomatic works on the same paired-end dataset :
https://usegalaxy.org:/u/lho-w/h/galaxy-main-trim

Please compare the Fastqc outputs in both histories.

Thanks a lot for your help.

Lena


#4

HI Bjoern, are you able to reproduce my error ?