Hi,
I have recently assembled exon-capture next-generation sequence data from two closely related species of deer against the cow genome. I assembled the next-gen sequences using Geneious, and output the results as a series of BAM files (one file for species and each cow chromosome, 60 file in total).
Geneious was really useful in identifying SNPs within exons within species. However, I now need to identify SNPs between the two species. There are far too many exon sequences to manually perform the comparisons necessary do this. Can anyone suggest a pipeline to automate this process?
I have recently assembled exon-capture next-generation sequence data from two closely related species of deer against the cow genome. I assembled the next-gen sequences using Geneious, and output the results as a series of BAM files (one file for species and each cow chromosome, 60 file in total).
Geneious was really useful in identifying SNPs within exons within species. However, I now need to identify SNPs between the two species. There are far too many exon sequences to manually perform the comparisons necessary do this. Can anyone suggest a pipeline to automate this process?