Just got back raw Affy Axiom SNP data from core lab, where do I start? (new learner)

Question

[devenvyas]

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 (20150422_103137_CHP_AxiomGT1.analysis_job, 20150422_103137_CHP.posterior.models, 20150422_103137_CHP_SnpSummary.analysis_job, AxiomGT1 All.GenotypeConsoleAnalysis.log, AxiomGT1.Genotyping Console.log, AxiomGT1.report.txt, AxiomGT1.snp-posteriors.txt, AxiomGT1.snp.summary.db, 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).

Thanks!

-Deven

Answer 1

[cpad0112]

Which chip exactly? Read this paper for basic work flows available and proposed work flow http://m.bioinformatics.oxfordjournals.org/content/early/2014/07/29/bioinformatics.btu486.full

[Simo]

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

Answer 2

[Simo]

Hi, I'm now working with the Axiom Human Origins Array, and I have to say that it seems to be very challenging! For the genotyping I have used the new Axiom Analysis Suite by runnung the Best Practice Workflow that integrates the QC analyses and the Genotyping itself. I also had to download the Annotation file in order to substitute all the propbe codes with the rorresponding rs ones. I also have found something really strange: some markers seem to have been tested twice, or three times sometimes, but with different genotyping results. So basically I have different doubles and triplets, Have you found something similar in your output? And have you found some more specific work about the analysis procedures? Not so many wors have been published about this Microarray, and the ones that are out there only say what they have done, and nothing about the procedures of analysis. Can you give some hint?

Thanks.