When ever I see bad bioinformatics, a little bit of me dies inside, because I know there is ultimately no reason for it to have happened. As a community, bioinformaticians are wonderfully open, collaborative and helpful. I genuinely believe that most problems can be fixed by appealing to a local expert or the wider community. As Nick and I pointed out in our article, help is out there in the form of SeqAnswers and Biostars.
I die even more when I find that some poor soul has been doing bad bioinformatics for a long time. This most often happens with isolated bioinformatics staff, often young, and either on their own or completely embedded within a wet-lab research group. I wrote a blog post about pet bioinformaticians in 2013 and much of the advice I gave there still stands today.
There are so many aspects of bioinformatics that many wet lab PIs are simply incapable of managing them. This isn’t a criticism. There are very few superheros; few people who can actually span the gap of wet- and dry- science competently. So I thought I’d write down the 5 bad habits of bad bioinformaticians. If you are a pet bioinformatician, read these and figure out if you’re doing them. If you’re a wet lab PI managing bioinformatics staff, try and find out if they have any of these habits!
Using inappropriate software
This can take many forms, and the most common is out-of-date software. Perhaps they still use Maq, when BWA and other tools are now far more accurate; perhaps the software is a major version out of date (e.g. Bowtie instead of Bowtie2). New releases come out for a reason, and major reasons are (i) new/better functionality; (ii) …read more
Source:: biomickwatson.wordpress.com
