Hi there, I am new to genomic sequencing but have a lot of experience using sanger sequence for cloning and to analyze spontaneous bacterial mutants (novel antibiotics). I need help.
I am currently trying to figure out how to use whole genome NGS sequence from Illumina's basespace to look for non-target-based mutations. I have data for the parent strain as well as several mutants.
I think I should be aligning the parent data to a published genome from Genebank or KEGG, and then aligning the mutants to the parent to look for mutations, rather than using de novo sequencing for the parent. Does that sound right?
I currently have active demos of DNA Star and Sequencher, and have performed the alignments I just described in both, only to find that there are hundreds of SNPs and idels of difference between parent and mutant strains. Clearly most of these are not real and need to be filtered out. How do I go about doing that?
Thanks for any help you can give me!
I am currently trying to figure out how to use whole genome NGS sequence from Illumina's basespace to look for non-target-based mutations. I have data for the parent strain as well as several mutants.
I think I should be aligning the parent data to a published genome from Genebank or KEGG, and then aligning the mutants to the parent to look for mutations, rather than using de novo sequencing for the parent. Does that sound right?
I currently have active demos of DNA Star and Sequencher, and have performed the alignments I just described in both, only to find that there are hundreds of SNPs and idels of difference between parent and mutant strains. Clearly most of these are not real and need to be filtered out. How do I go about doing that?
Thanks for any help you can give me!
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