Hi, I have E.coli genome re-sequencing data. I want to use this data to find or predict any result which related to drug resistance. I haven't had any experience about this . And now all I think is align re-sequencing data against to reference genome and get the SNPs file, So what should I do next ? I have no idea about this. Does anybody could give my some suggestions or hints? Any useful ideas or clues would be appreciated.
So what should I do next ?
Find the consequence of those SNP's using a variant effect predictor program (e.g. Ve!P). Once you identify genes that may have interesting changes that could relate to the drug you are looking at you can do more extensive structural bioinformatics investigations to see how the SNP's may be affecting structure of the protein.