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Answer: visualize GSEA
by
bk11
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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 > …
Comment: Differential Expression Analysis using DESeq2 in R
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swbarnes2
14k
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?
If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
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![Here is the code I am using for the analysis][1]
[1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
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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?
by
curious
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According to the link:
"When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
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nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
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e.r.zakiev
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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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GenoMax
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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…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
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Okay, that shows us the problem, but not what we need to solve it.
But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★
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In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1].
[1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
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Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★
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In Plink, A1 is usually a minor allele and A2 a major allele.
.frq (basic allele frequency report)
Produced by --freq.
…
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