I am new to Galaxy and have been trying to trim off the adapter and overhang, followed by build a collection, flatten and QC. But Trimgalore is not accepting any fastq paired collection. What is the other way to go ahead with this?
You are very close, and have hopefully found this already in other posts!
Why the tool does not recognize the inputs?
- Notice how the input area is clarifying the datatype of the input files it is looking for: fastqsanger or fastqsangergz
- Then, see how the datatype is currently assigned to the collections in the history: fastq.gz
- That is creating a mismatch, so the tool cannot “see” the collection as a valid file input type
What to do this time
- Click into the pencil icon in the upper right corner of the collection dataset in the history. You can update the assigned datatype on the Edit Attribute forms that will display in the center panel.
What to do next time
- Let Galaxy “autodetect” the datatype when Uploading files.
- If the guess is wrong, that can be an important warning about some kind of formatting problem or a partial upload.
- For more exotic datatypes, you can directly adjust to the correct format after Upload by using the pencil icon, or can assign during Upload. But for reads, autodetect should work great!
Why does it work this way?
There were several different fastq read formats early on, and that had scientific consequences depending on the quality score scaling actually used inside the file. The scaling sometimes had to be adjusted. But now, most protocols use the Sanger Phred +33 scaling, and the fastqsanger datatypes are usually the best fit. Galaxy still does a quick “double check” … since if incorrect, that can really skew the results or lead to strange tool errors.
We have many more resources about this topic with FAQ details and Tutorial examples. I added some tags and this good place to start as needed → Getting Data into Galaxy