The single most important thing you must do when considering outsourcing your bioinformatics work is: vetting the bioinformaticians thoroughly. Think this way: you will be spending thousands of dollars (or more) letting someone who is non-local, whom you likely have not met before - complete a component of your research project for you. You need to look at their credentials closely, examine their related experiences, ask for references, talk with them about your project - not just the bioinformatics portion, but the entire project - and probe them with questions to determine whether they actually understand what you say. You should not sign on an agreement to have them do the work only because they say they can do it, or because they provide a heavily discounted quote. It is true that mistakes made in hiring an outsourcing bioinformatics team will not be as bad as ones made in hiring a local person on your payroll. However, beware that hiring a wrong bioinformatics teach will not lead to wasting of your research funds, but could also cause (potentially devastating) delays in the progress of your project.
There is another reason why you should vet the bioinformatics service teams thoroughly: bioinformatics expertise is in high demand, and bioinformatics training programs all over the nation are having a hard time producing enough qualified bioinformaticians. It is not uncommon for some teams to use underqualified persons. I know of more than one institutional sequencing core facility equipped with “bioinformaticians” who are essentially young folks with a recently obtained bachelor degree in biology followed by a few weeks of bioinformatics training: Seriously, you might be better off having your own students do the bioinformatics work than “outsourcing” the work to those kids… I also know of a few local bioinformatics companies headed by young guys so inexperienced that they would barely qualify to be assistants to a Lead Bioinformatician at AccuraScience. I have no doubt that over time, these young guys will get experienced and more confident in what they do. But I do have serious doubts as of what would come out of a bioinformatics project led by these young guys at their current stage - without oversight by a more senior person.