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Mikl1984 — Sun, 18 Jan 2026 09:54:16 +0300

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(a) install WGSE.bio
(b) download the FASTQ files
© open WGSE.bio and select an output directory (create it in the same folder as the FASTQs and name it "WGSEv4")
(d) go to third tab (analyze), and under FASTQ then select "Align"
(e1) select both FASTQ files, and then
(e2) choose your reference genome (hs37d5 is the best, human_g1k_v37 is what tellmeGen used to create the VCF, hs38 best if you want to also submit to yfull)
(e3) in a file select pop-up in the output directory, you need to type in the a final file name ending in ".cram" (or ".bam"). Often best to use the same base name in the FASTQ files — your test id. So something like ULMEDCBA3296.cram and then hit "Save"
(f) wait 4 to 180+ hours; depending on the resources of your desktop
(g) when done, the ".cram" will be loaded
(h) hit the "Index" button (wait another hour)
(I) hit the "Stats" button just to confirm everything looks correct (another hour with CRAM unfortunately)
(j) on the second tab (Extract Data), hit the "microarray RAW" button to bring a new popup
(k) hit "Generate" and wait a few hours
(l) when done (status pop-up gone, program responsive again), you should find several zip'ped ".txt" files in the output directory you can use with sites that take microarray files. Try to use the CombinedKit if they take it. It is less than a minute to generate the others on that microarray pop-up if you need them (once the CombinedKit is generated and found again).
(m) Exit WGSE
( n ) I usually like to move the .cram and .crai file to the same place as the FASTQs and VCF. They are now source files you will use again and again. You can safely delete the FASTQ files if you are space constrained as they can be easily recreated from the CRAM. The CRAM is the same or smaller size than just one of the two FASTQs. 20-30 Gigabytes.
The source directory of the FASTQs, the "Temp" directory and the output directory can all be on different disks. "Temp" is the most important as it will need 500+ GB of free space and should be your fastest disk. Output will temporarily need 100 GB or so but only 25 GB once done. Lots more detail in the WGSE User Manual

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Mikl1984 — Wed, 05 Nov 2025 21:21:45 +0300

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Mikl1984 — Wed, 24 Sep 2025 22:46:49 +0300

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The raw data is provided in FasQ and VCF format