To elaborate on the title...
After filtering from 19,578 to 2209 binary SNPs, I converted the genlight object into a structure format to be used for fastSTRUCTURE in the LEA package. I noticed when running a cross-entropy test that it increases to 5372 loci. (Side note, the species I am studying is an aquarium fish so there is a lot of genetic inbreeding, the reason for such low SNPs)
Is this normal when running this analysis? I am attaching my script below. I would greatly appreciate any help!
glxh<-gl.read.dart(filename=" NoMolly",covfilename="metadataallnomolly.csv")
save(glxh, file="xhell.rdata") load("xhell.rdata")
gl.report.monomorphs(glxh)
glxh1 <- gl.filter.monomorphs(glxh)
gl.report.callrate(glxh1, method = "loc")
glxh2 <- gl.filter.callrate(glxh1, method = "loc", threshold= 0.82)
glxh3 <- gl.filter.secondaries(glxh2)
gl2faststructure(glxh3, outfile = "glxh3.str", probar = TRUE)
struct2geno("glxh3.str", ploidy = 2, FORMAT = 2)
project = snmf("glxh3.geno", K = 1:20, entropy = TRUE, repetitions = 10, project = "new")
