How to incorporate the reference into SNP tree

[NGS group]

Hi everyone,

I am trying to build a SNP tree. The principle is to extract SNPs from each sample mapped to the reference to get a pseudo "SNP genome", and then multi-alignment will be performed with all "SNP genomes". However, there is no SNP can be extracted from the reference mapping to itself. Therefore, the question is how to incorporate the reference into the SNP tree?

Thank you very much in adavance!

Victor

[NGS group]

No one can give me any suggestion? It seems that such kind of questions always have no answer in this forum.

[rhinoceros]

Originally Posted by NGS group

No one can give me any suggestion? It seems that such kind of questions always have no answer in this forum.

It seems to me like a simple literature search (or even google) would answer your question, but perhaps I'm wrong..

To be honest, I don't see how your method is going to work. I mean, as far as I can tell, you're extracting all the nucleotides that differ for all samples vs. reference, so you end up with files that differ in nucleotide counts. How are you going to get anything meaningful out of those files? Or are you recording also the loci of all the snips? If yes, then why not just extract those loci also from your reference?

p.s. Almost all of my questions here have gone unanswered, but I take it as a compliment

[westerman]

Originally Posted by rhinoceros

p.s. Almost all of my questions here have gone unanswered ...

That is because you ask hard questions. Or, better yet, figure out the answer on your own.

As for NGS group's question, I agree with rhinoceros -- just extract the loci from your reference. Although I would do this only when two or more of the other samples have the loci in common.

The way I think about this is, if I have three sequences/samples:

#1 (the reference; presumably created from multiple other samples)
#2
#3

Then if #2 has a SNP as compared to #1 I want to use that. Ditto for #3 vs. #1. But I can also reverse the procedure via make a pseudo-reference from combining #2 and #3 and then compare #1 to the #2/#3 combination in order to find SNPs in #1. The way to make that pseudo-reference is to look at the #2 vs. #1 and #3 vs. #1 SNPs and only take the ones in common.

Whew, I hope the above logic makes sense. I can visualize in my own brain but it is hard to write down.

That above pseudo-reference is similar to 'NGS group's "SNP genome" only instead of using all of the samples to come up with SNPs from the reference I am only using two (or maybe three) other samples in order to determine the reference's SNPs.

It is sort of like physics -- one's reference is relative.

[themerlin]

Victor,

If you are doing a SNP analysis against a reference, just include your reference as an external genome, as well as the reference, and it should be processed with the rest of your external genomes and show up in your tree.

Jason