FASTQ files come in various flavours. They differ in the encoding scheme they use. See our QC tutorial for a more detailed explanation of encoding schemes.
Nowadays, the most commonly used encoding scheme is sanger. In Galaxy, this is the fastqsanger datatype. If you are using older datasets, make sure to verify the FASTQ encoding scheme used in your data.
Be Careful: choosing the wrong encoding scheme can lead to incorrect results!
Tip: There are 2 Galaxy datatypes that have similar names, but are not the same, please make sure you fastqsanger and fastqcssanger (not the additional cs).
Tip: When in doubt, choose fastqsanger