Hello! I am having some trouble figuring out how to use Salmon. I have around 30 different samples which I trimmed using bbmap then aligned them using STAR. I have all of the BAM files from this alignment. Should I merge them all before running Salmon or because they are all unique samples, do I run them separately? I also aligned them to the UMD3.1 cattle genome. Is this ok for Salmon or should I align it to a different reference? I am very new to all this and trying to teach myself as I go. So if anyone has any other sites that could help me out, that would be great!