Using the RNA seq data and have performed de novo assembly with non-model species. I have used a lot of tools on galaxy and reached the point where I have a list of about 80,000 SNPs. Now in order to validate the SNPs I need a powerful tool. Is there a method in galaxy to fetch sequences around SNPs? I saw a tool "flanking sequence"in genome diversity suite but unfortunately I am not able to create gd_snp file which seems to be a requirement to use the tool. Any help on how to get sequences from SNP list?
I have nucleotide sequences of validated markers. But how should I be using this to compare the sequences from SNP list if I don't have my SNP sequence at all.
Thankyou in advance.