Trimmomatic tool for paired end sequences on galaxy

Any ideas as to why when I try to click the paired end (as collection) option from the drop down menu in the trimmomatic tool my paired end data collection doesnt appear as an option and only single ended is an option? Thanks in advance

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Welcome @Niamh

The Trimmomatic tool at is functioning correctly for all of the input “select” options.

Exact tool version: Trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.38.0)

Maybe your paired-end dataset collection has some problem that needs to be corrected?

This history has examples of individual plus various data collection groupings for fastq data. Maybe it will help to compare your collection data structures with those in the shared history?

Collection tutorials: Also, many other tutorials at this site include data collection creation/usage. I’ve also added a tag to your post that links to similar prior Q&A.


Hi Jenna thanks for the reply, I think it must be my dataset or something I am missing. I have been told I’m working with paired end reads which is indicative of the library prep methods used. But it appears to me when I upload them on galaxy I’m working with read 1 of a pair. I thought they could be combined and I could split them but I don’t think they are.

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Expand a few of your initially uploaded datasets and examine the content.

Some things to check for:

  1. Is the “datatype” for the fastq data set as fastqsanger or fastqsanger.gz? Or something else?
  • Galaxy will autodetect fastqsanger for fastq data that is originally uncompressed and will uncompress then assign that datatype to fastq that is originally compressed.
  • To preserve compression, the datatype fastqsanger.gz can be assigned. But you should double check the data really is in that format (fastqsanger) AND is actually compressed.
  1. Now click on the “eye” to view the content:
  • Do you see only forward reads?
  • Or only reverse reads?
  • Or are both forward and reverse reads combined (interleaved/interlaced) into the same single file?

That review should help to determine the data you have now, and how to get it formatted in the correct way so Galaxy can use it.

These FAQs cover the details:

If you get stuck, we can troubleshoot from here. Please describe the current assigned datatype and the data content itself. Screenshots can sometimes help. If more info is needed after that, we can keep following up until it is right.