Entering edit mode
10 weeks ago
Nuglozeh
▴
10
Hi everyone
Can somebody direct me on how to draw an SNP profile on human chromosome 1? I have run exome sequencing using genomic DNA from patients suffering from diabetes. After bioinformatics analysis, we generated an SNP profile for all human chromosomes. We would love to compare these profiles to normal human chromosomes, in another to SNP profiles amating from hg38. Can somebody help me?
Do you mean a "Manhattan plot"?
It's not really clear what you want to do. I can definitely help you if you want to accurately call variants on human chr1, but is that what you want to do? It's not really clear. I've never heard of a "SNP profile" and I can't imagine how it would be useful. Also, there's no such thing as a generic "bioinformatics analysis". That's like using a tricorder to diagnose problems.
What can be useful is comparing specific SNPs to other specific SNPs known to be disease-related, or mutations in related genes (they do not need to be SNPs, and indeed, indels tend to be more serious). Once you have a clear picture of what you want to accomplish, it's possible to lay out a plan to do it, so I suggest you consider it a bit and then post again.