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Answer: The GDC Legacy Archive is retiring soon.
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Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
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(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII )
You need to use --chr-set, not --allow-extra-chr, to specify…
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This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
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I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
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Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that?
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![Here is the code I am using for the analysis][1]
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In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
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Comment: Easy way to find out which allele is minor allele from bed file?
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According to the link:
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obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
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You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
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![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
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Okay, that shows us the problem, but not what we need to solve it.
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