SNPs confusion?

[arkilis]

I have four samples from diff animals. I used the novo snp to do the snp analysis.

First time, I put all the sample data together and do the align. There are 5 snps found (QS>25).

Second time, when I do the align separately. No SNPs found at all. Any ideas/thoughts?

thx

[jimmybee]

Im sorry but unless you give us information about what you did, we will have no way of helping you.

What commands did you run? Go through step-by-step. What reference sequence were you using? etc etc