Weirdly enough, my single end reads are on two separate fastq files. Do you know why this happens? Can I rely on them or must I make a single file for mapping with tophat2? I saw that paired end reads must remain on separate files, but what about the single end?
Check with the sequencing centre, they may have run your sample in two different lanes or on different days. For mapping I would suggest keeping them separate for now if this is the case, you want to be able to determine if there are any batch-effects.
Even if you do have paired end data, it would pose no problem to pass these files both as fragment reads to an aligner. If you do have paired reads, you might see that the end of the read names in each file are appended with "/1 or /2" or a space and then "1:... or 2:...".