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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
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750
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
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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…
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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
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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
★
2.4k
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
▴
750
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
★
2.4k
In Plink, A1 is usually a minor allele and A2 a major allele.
.frq (basic allele frequency report)
Produced by --freq.
…
Comment: Raw counts using stringtie
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GenoMax
142k
> Error parsing strand from GFF line
Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
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dsull
★
6.0k
I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
Comment: High Malat-1 expression in single cell data
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carolofharvest
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Thank you for sharing.
What are your thoughts on the genes Gm42418, AY036118, and Gm26917? Some articles suggest that clusters with an abu…
Comment: Do I need to go back and filter my long-reads?
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> I think I will filter the reads ultimately.
If your data was not run and basecalled using the same exact version of pore/software for a…
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Ram
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What is `stringie.sh`? Try `./stringtie.sh -h` and then `more stringtie.sh`.
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