My understanding is that it is important to have PCA's based on cases and controls specific to the phenotype to be analyzed in GWAS. I have fashioned the appropriate files (I think), consistent with examples online, but I'm having difficulty running it in DNANexus - I can't run all 400,000 subjects at once, so I picked out 40,000 (the maximum number) and pruned SNPs, but I'm unsure how to run the 40,000 then project it to the 400,000 total subjects. Has anyone had experience with Eigensoft in DNANexus?
Thanks for your help.
Royce
on array data. I'm looking to use the CONVERTF to convert plink files to Eigensoft files. I've tried creating .ped files, but somehow I get multiple errors. Thanks for answering.
Can you please post the specific errors that you are getting?
From the EIGENSOFT FAQ page it looks like memory is the main limiting factor when scaling up the sample size. What instance did you try when you were running EIGENSOFT? Maybe it would help to increase memory size (e.g. using mem2 in instance type).
Regarding projecting results from 40000 samples to the rest of the sample set, you can use -w flag to smartpca.perl. See documentation.
Hi, Anastazie:
Thank you for answering. I used the Eigensoft Tool in the Tools library, using files in my March 25, 2022 /Data folder. I have an entire slew of job failure reports, and it is case #00034608 in DNA_RAP. They have been trying to help, but no joy. I have attached the most recent email from July 9, 2022
Royce
Good morning, Jamie, et al:
I am inquiring as to the progress of the above error. This is about EIGENSOFT, a tool provided in the DNA-Nexus program.
; I?m just asking whether there is some progress or resolution so that either I can use the file .extensions as indicated in the EIGENSOFT program
https://ukbiobank.dnanexus.com/panx/tools/run/app-G4Yxp3QJ57J1BGgF0x5YJGqV/analysis-inputs
which were all created using plink within the dnanexus site, or that there is a convertf program available either within the eigensoft program, or that I can use to convert to prescribed filetypes by eigensoft.
Thanks for your help on this.
Royce
Community members do not have access to DNAnexus' support system. Can you please share relevant details from your communication with the support team? It is more efficient to use only one channel to solve your issue (either support team or community forum).
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Are you running EIGENSOFT on array or WES data?
on array data. I'm looking to use the CONVERTF to convert plink files to Eigensoft files. I've tried creating .ped files, but somehow I get multiple errors. Thanks for answering.
Can you please post the specific errors that you are getting?
From the EIGENSOFT FAQ page it looks like memory is the main limiting factor when scaling up the sample size. What instance did you try when you were running EIGENSOFT? Maybe it would help to increase memory size (e.g. using mem2 in instance type).
Regarding projecting results from 40000 samples to the rest of the sample set, you can use -w flag to smartpca.perl. See documentation.
Community members do not have access to DNAnexus' support system. Can you please share relevant details from your communication with the support team? It is more efficient to use only one channel to solve your issue (either support team or community forum).
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