I have done an experiment whereby I have collected all of my samples, and done some of the pre processing required. These samples were then sent to an external commercial lab for further processing and the raw data returned to me for analysis and write up.

My question is - Can this data be used in my thesis as an external lab was involved? I think it's ok, but just want to get some people's opinions on this. I am 1 year 3 months in to my PhD and this represents my first real data set.

If this data is a genome sequence then this is fine.

It is pyrosequencing data. The company also did some of the bioinformatics?

I think it's ok as you make it clear what you have done and what they did. You just need to make sure you are still making a substantial contribution I guess.

Hi MicroWest,

I did this, too, for one of my thesis chapters. I designed the experiments, prepared the samples, handed them over to a collaborator who produced chromatograms and numerical data, and then I did the data analysis and wrote it up.

Yep. It's still your study. You just asked someone else to use an established [presumed] method which was unavailable in your lab, and for which they were [presumably] paid. If you initiated the collaboration (as I did), it might count in your favour, as it shows you've got the gumption to do so.

I would add a cave, however: if a paper is coming out of this, sort out authorship, especially first authorship. I've recently been having problems over this, though not actually because of my collaborator. He's cool, semi-retired and has a s***-load of papers. Nonetheless, my supervisor decided - off his own bat - to offer him co-first authorship. I tore him off a strip and he's had to back track. Hopefully, he's suitably embarrassed. But just be mindful of it...

Thank you very much, I really appreciate it. It was for my first set of samples from my first exploratory experiment, and indeed it was using next gen sequencing apparatus that we didn't have at my institution at the time. We are however getting this apparatus shortly, so I should be able to prepare the next samples for my next chapter myself. It was more to see if this apparatus was the correct one to use moving forward into my next experiments, but this data should definitely form my first chapter.