I would like to ask several questions regarding how to compare 2 genomes in order to find differences: Assume I have 2 dataset of sequencing data from 2 plants of a same species (e.g. arabidopsis) - 1 plant has normal phenotype, the other has disease phenotype. Theoretically, the disease phenotype is known to be controlled by a single gene, and these 2 plants should have similar genome accept the region that responsible for the phenotype. I would want to somehow compare the 2 genomes to find out differences between 2 plants (in order to find the disease gene).
I'm a newbie in Bioinformatics (also newbie of Biostars), I do not know where to start. Would you mind providing me some guides to help me find an approach for my problem? - Projects or publications that have similar object; Documents, internet or books, that I should read; Maybe a suggested pipeline would be great...
Thank you for reading.
P/S: And I am sorry if my english is horrible.