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dbailleul / RClone

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SNP format input for RClone #1

Closed mstagliamonte closed 5 years ago

mstagliamonte commented 6 years ago

Hi, Thank you for RClone!

I was reading the manual, and I would like some more detail regarding the input formatting in case of SNP data. is it the same as microsatellite, just replacing the repeat number with the nucleotide allele?

Kind Regards, Max

dbailleul commented 6 years ago

Hi Max, thanks for using RClone ! I'm not really sure to understand your question ... is it related to genetic distance ?

mstagliamonte commented 6 years ago

Hi, DBailleul,

I was trying to use RClone with SNP data, i.e. genotypes would have nucleotides rather then repeat lengths (e.g. A/A, G/C, etc...). I was wondering how to format my input. Can I just use characters? Something like this: Two samples, two loci: Sample1: (A/A, C/G) Sample2: (A/T, G/G) would become:

                      Locus 1_1      Locus1_2          Locus2_1        Locus2_2
Sample1                A                  A                 C             G
Sample2                A                  T                 G             G

Is that correct? Or is RClone better suited to analyze microsatellite data only?

Thank you for your kind attention, Max

dbailleul commented 5 years ago

Theorically, you should be able to use letters (A/T/C/G) instead of numbers (101/000) with RClone. But just to be sure, I would advise to change A = 101, T = 102, C = 103 and G = 104 "just in case".

RClone is suitable to handle SNP data. The only problem is that I've never finished to implement missing data as true missing data (ie not another allele as "000" would be considered now). You know how postdoc are ... but I hope I will be able one day.

mstagliamonte commented 5 years ago

Yeah, I know ;-)

Thank you for your help, and good luck. Max