Hallo! I am still not grounded in this field and I have a deadline fast approaching with basically no how to proceed. I am working with nanopore data trying to identify the species of mosquitoes, their last blood meal and check if they have kdr resistance. I initially used kraken for the metagenomics classification using the whole genome sequences of the mosquitoes. However, my supervisor suggested I use a specific gene, which is the cox1 genes. I am getting confused on what to do. Truth is, I have not made much progress and I sincerely need someone probably proficient in this field.
I grasp things easily but I do need to what to do and why I am doing it.
Ofcourse I am willing to pay by the hour for the help.
I will appreciate a feedback.
Thank you
I can be reached at doppelganger1030(at)yahoo(dot)com
Talk to your supervisor. Express the need of help. It is their job to take care of that by establishing a collaboration. Don't pay from your own pocket. See whether there are any online courses (and be it paid one) and let your PI pay to give you the training you need.
Thanks for your response. However, it's for my thesis. And the development is personal hence why I do not mind paying for it. Thanks again!
I would argue this could also be seen as professional development rather than personal. Supervisors should be there to support the development of their students and staff at all levels. In my experience, they usually are, but this isn't always true. A little late, but you probably should have indicated that you were struggling to them before your deadline was so close.
The first place to look is in the literature. The cox1 gene is one of a handful of markers often used to draw phylogenetic inferences from in mosquito species. See this as an example. My guess is they are suggesting you use this gene to identify the different species, but not the other traits you are investigating. You could extract cox1 from each of your samples, include reference versions of potential species in your samples, and create a phylogeny using something like RAxML.
Thank you!!! The literature is helpful.
Thanks again