4.2 years ago by
WCIP | Glasgow | UK
Here's my take on this, partially repeating other answers:
- Basic statics: At least to understand why replication matters, why a p-value of 0.001 is not too exciting if it comes from a batch of 20000 tests.
- R programming: At least to be able to follow a Bioconductor vignettes and replace Excel for common tasks like sorting and subsetting a table, plotting.
- Unix skills: Able to move around files and dirs (
cd, ls, mkdir, etc) and Unix tools to manipulate files (
sort, cut, awk, etc). Able to install and launch a command line program (provided that there are no quirks in the installation process).
- Tools for bioinformatics: Almost for sure for NGS you need
bedtools or equivalent. Understanding of common file formats: SAM, bed, gtf.
- Good house keeping: Document what you have done, just like in a labbook. Avoid duplicating data, copying files and keeping stuff "just in case..." (some concepts from the relational database world would be handy).
Some scripting language like python would be a plus but with R+Unix tools you already go a long way.
I wouldn't require all the stuff above, but at least I would ask for a willingness to learn.
In general, you would need enough understanding and familiarity to be able to present your problem to "the expert" (say the pure statistician/mathematician/computer scientist) and be able to make use of the answer. Essentially be able to communicate with non-biologists.
I'd like to disagree with Michael Dondrup when he says biologists shouldn't do (NGS) analysis. I think the biologist is the one that best understands the problem so he/she is in the best position to ask meaningful questions and spot features in the data attributable to potentially interesting biological or technical causes. Then of course, you still need "proper" bioinformatician in the team, but I think you get a lot done with basic expertise from the list above.
(By the way, I don't claim to be an expert. In fact the distance between what I know and what I should know seems to keep increasing with time. Sigh...)
modified 4.2 years ago
4.2 years ago by
dariober ♦ 10.0k