I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in order to observe differential gene expression. I have been messing around with Drosophila melanogaster experimental reads from the EBI SRA site.
Most experiments are labeled as paired-end reads, however when I go to download the data there is usually only one file (some do have two). Does the one file mean that both ends are in the same file, and if so in what format? Aligned next to each other in one long read? Stacked on top of each other? Is there a way to check if reads are paired-end in one file? Or split paired-end reads that are all in one file into single-end reads?
Thank you in advance for any help with this issue.