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Old 07-11-2014, 03:21 AM   #1
Corydoras
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Location: Norwich

Join Date: Jan 2014
Posts: 20
Default Identifying unique alleles/haplotypes for contigs

Dear All,

I have successfully created contigs using paired-end RAD data, and equally successfully mapped raw reads from different species back to these contigs. So far so good and I am loving my bioinformatics adventure!

When I visualize these contigs (for instance by using tablet), I can clearly distinguish alleles, for instance it looks something like what I have attached.

I have a list of several hundred contigs of interest that i want to compare between two species and I want to quantify the number of alleles I have per contig. I have trouble finding a way of doing so? Everything seems to focus on individual SNPS, but as above I am looking for a way of saying at this contig there appear 2 unique alleles/haplotypes, at another contig I have 3. Could anybody help me please with some pointers?

Many thanks in advance!
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