Hello, I just got back SNP array data for 93 samples and 2 positive controls (94th sample failed) for the Affymetrix Axiom Human Origins array for human pop gen analyses.
I got back one zip file with a genotyping array too big to possibly read with apparently 633998 really long lines (per 'wc -l' which corresponds with the number of SNPs)
The second zip file has ARR and CEL files along with xls files with call rates and Dish QC, Log Difference QC, AT Channel FLD, and GC Channel FLD values.
The third zip file has CHP files as well as other various small and large txt files (
AxiomGT1.summary.txt, and one
AxiomGT1.chp file per sample).
I am completely new to Axiom data, so I was wondering if someone could help me figure out what I am supposed to do first. The first things I want to do with the data are run some PCAs and STRUCTURE analyses followed by calculating f4 statistics (i.e., estimate Neanderthal introgression).
I'm working with the Axiom Genome_Wide Human Origins 1 Array.
By the way, thank you for the suggestion, but since the new Axiom Analysis suite has been released, it is possible to carry on all the analyses described in the paper just using that tool. The problem is the post genotyping snp filtering. If you have some information in dealing with this specific Array, could you give mi some hint? Thanks a lot