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Old 01-19-2018, 09:13 AM   #1
SDK
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Location: Canada

Join Date: Jan 2014
Posts: 17
Default Program to make consensus and call SNP?

Hello All,

I've got 2 distinct but related problems...well 3 problems if you count that I'm not a bioinformatician! I've just completed a pop. gen. microsatellite study using the MiSeq. I used a program to call the microsatellites and it did an excellent job. I think my questions probably have simple answers, but I'm a taxonomist, not a geneticist.

Problem 1: In addition to the microsatellites, I also designed and ran 4 small fragment (<150b) mtDNA loci. When you look at the read files there is obvious variation within one individual from PCR/Sequencing error. I have about 1200 samples and some individuals have rather large depths. How can I most efficiently create consensus sequences for each of these 1200 samples?

Problem 2: In addition to the microsatellites, I also designed and ran one locus to amplify a small fragment of the 5.8S for molecular species verification. There are 3 species which appear similar but can be separated using the 5.8S due to 2 SNPs. What is the best way to make a consensus sequence from all of the reads and to call the two SNPs? I have GENEIOUS but I'm not sure this will do the trick.

Thanks for any insight you can provide and apologies if it's a noob question!
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consensus, microsatellites, miseq, snp calling

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