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!
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!