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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
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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?
If…
Comment: Differential Expression Analysis using DESeq2 in R
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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…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
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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…
Comment: Converting CRAM to FastQ
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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…
Comment: Converting CRAM to FastQ
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Maverick
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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
14k
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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