I am beginning to working on a project that eventually should be able to do multi sample SNP calling in plants.
I am a novice in bioinformatics and never used any Linux or Python, that is something i am also currently learning on how to use software in a Linux environment and learn to use python. I did use software like UGENE in the past.
I have done SNP calling before but only on a small scale regarding a bacterium and this was a project i had to do for a course in college. that also how i eventually wanted to go into bioinformatics. My formal back ground i biomedical Sciences but i want to go more into bioinformatics instead of the lab.
Now for my project, I have so test one diploid plant and one polyploid plant.
the last days i have reading this website and been searching for all kinds of questions regarding multisample of single sample SNP calling. and SNP calling in general. I also have been looking for papers and looking for videos on youtube regarding this topic. This was all to get a more general idea of the topic and to see where in lack knowledge.
Some of the papers i have read( thanks to this website) are:
With reading all kinds of papers i did the last days i find one thing more difficult to find. and that is finding a paper that applies to plants instead of human or mammals.
before i make any further plans on what software to use of even how to use them i would like to find some information or papers that discus SNP calling (on a large scale) for plants.
Should i also start thinking already on how many haplotypes the plant has when i want to make a pipeline/work flow or using existing pipelines/work flows in for example galaxy. Or is that something i don't have worry about?
Maybe Someone here can point me in a good directing on where to start reading for SNP calling in Plants and if there are things i have to look out for compared to SNP calling to humans/mammels.
Maybe this story i a bit vague, if you have any questions i will be happy to answer them.
KInds regards Covux