Issues with Test Analysis Output in MixDeR

[More92]

Hi,

I am trying to use your deconvolution software. As a first approach, I ran the analysis with the test data available in the "testdata" folder. The analysis seems to have completed successfully, as no errors were reported. However, the output folders are empty and do not contain any results.

I am attaching the log file so you can see how I executed the analysis. Additionally, I would like to know if this software can only be used with SNPs from the ForenSeq® Kintelligence kit or if it is also compatible with other SNPs.

Setting Value MixDeR Version: 0.7.4 EuroForMix Version: 4.2.4 Path to sample manifest: C:/Users/stefa/Desktop/mixder-main/mixder-main/tests/testthat/testdata/samplemanifest.txt Path to mixtures: C:/Users/stefa/Desktop/mixder-main/mixder-main/tests/testthat/testdata Output path: C:/Users/stefa/Desktop/mixder-main/mixder-main/tests/testthat/testdata/snp_sets/output/ Number of SNP sets: 10 Minimum number of SNPs: 6000 Static AT: 10 Dynamic AT: 0.015 Running mixture deconvolution: FALSE Running unconditioned deconvolution: FALSE Running conditioned deconvolution on references: FALSE Method run post deconvolution: Create GEDmatch PRO Report Filtering SNPs if allele 2 is missing? FALSE Allele 1 probability threshold (for GEDmatch PRO reports): 0.99 Allele 2 probability threshold (for GEDmatch PRO reports: 0.6

Thank you for your assistance.

[rnmitchell]

Hi- sorry for the delayed response. In the Shiny app, you need to select the deconvolution analysis type by checking either conditioned or unconditioned (or both!). That should fix your problem.

MixDeR is designed specifically for the Kintelligence assay, however, it doesn't mean it can't be used for other sets of SNPs but will take some engineering. You (or a bioinformatician) could likely edit the code to allow for other SNP sets to be utilized it's just not something we've tested or performed yet.