If you are working at a larger academic institution, chances are you will find one or more bioinformatics faculty members in your institution. Would collaborating with them be a good option for you? My advice is, take a look at their research interests, and see if synergy could be formed between your research and theirs. For instance, if one of these local bioinformatics researchers is interested in developing more accurate peak calling methods for ChIP-seq data, and your research project is going to generate a bunch of ChIP-seq data with some unique characteristics, then there is the potential for synergy to form between the two labs, and it could turn out to be a good local collaboration.
If, on the other hand, there is quite some distance between your research interest and that of the local bioinformatics researcher, my recommendation is: do not forge a “collaboration” when all what you want is a "service": it will not play well. Put yourself in his/her shoes, and try to understand that everybody has his/her own priorities.
Academic collaborations always have some intricate elements associated with them: You want to publish the results first, but he/she wants to publish the method first. You want your student to be the first author of this article, yet he/she wants his/her postdoc to be the first author instead. You want to finish up writing of this paper quickly, but he/she has to focus on a grant application. Notwithstanding that very productive collaborations can be - and have been established between experimental researchers and bioinformatics researchers in many different places, it is important to recognize these intricacies. There will be times that after thinking these through, you would determine that it is better to avoid all of them and go down the easy path - to have a commercial entity to take care of your bioinformatics need.
About the Author: Justin T. Li obtained his Ph.D. in Neurobiology at the University of Wisconsin-Madison in 2000, and a M.S. in Computer Science at the University of Houston in 2001. Justin served as an Assistant Professor in the Medical School at the University of Minnesota Twin Cities campus between 2004 and 2009, and as Chief Bioinformatics Officer at LC Sciences (Houston) between 2009 and 2013. In June 2013, Justin joined AccuraScience as a Lead Bioinformatician. In his career in the academic as well as in the private sector, Justin has published ~40 research articles in various research domains, and led the development of 12 bioinformatics database and web servers. More information about Justin can be found at http://www.accurascience.com/our_team.html.