Finding mutations in MiSeq data?
Hello,
First time posting here. I'm a beginner in computational biology. I am working with a bacterium that already has a reference genome.
Basically, I have a mutant of that bacterium that lacks a certain protein. In my experiments, I saw a peculiar phenotype with certain colonies of the mutant. I think these colonies might have some interesting mutations in them.
I sent the parent mutant, as well as the colonies of that mutant that exhibited the interesting phenotype for MiSeq sequencing.
I have 2x301bp paired end data for the mutant parent as well as the colonies. How would I go about finding the mutations in the colonies compared to the mutant parent?
Here is what I have done so far using Geneious:
1.) I selected the two read files for the mutant parent and colonies and set paired reads with the insert size I got from the sequencing company.
2.) I mapped the mutant parent and the colonies to the reference genome of my organism using Geneious.
3.) I then did "Find Variations/SNPs" on Geneious on the parent mutant as well as the colonies.
Doing this, I got csv files with a list of mutations. The first file I got is the mutations in the mutant parent compared to the reference genome. The other files I got are mutations in the colonies compared to the reference genome.
Am I on the right track? Is Geneious the best tool for me to find mutations? Is there anything else I should be doing?
First time posting here. I'm a beginner in computational biology. I am working with a bacterium that already has a reference genome.
Basically, I have a mutant of that bacterium that lacks a certain protein. In my experiments, I saw a peculiar phenotype with certain colonies of the mutant. I think these colonies might have some interesting mutations in them.
I sent the parent mutant, as well as the colonies of that mutant that exhibited the interesting phenotype for MiSeq sequencing.
I have 2x301bp paired end data for the mutant parent as well as the colonies. How would I go about finding the mutations in the colonies compared to the mutant parent?
Here is what I have done so far using Geneious:
1.) I selected the two read files for the mutant parent and colonies and set paired reads with the insert size I got from the sequencing company.
2.) I mapped the mutant parent and the colonies to the reference genome of my organism using Geneious.
3.) I then did "Find Variations/SNPs" on Geneious on the parent mutant as well as the colonies.
Doing this, I got csv files with a list of mutations. The first file I got is the mutations in the mutant parent compared to the reference genome. The other files I got are mutations in the colonies compared to the reference genome.
Am I on the right track? Is Geneious the best tool for me to find mutations? Is there anything else I should be doing?
Comment