User: haneenih7

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haneenih710
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Posts by haneenih7

<prev • 14 results • page 1 of 2 • next >
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What is the diffeernce between singletons and doubletons - VCFtools
... Hi all, I've used vcftools ( --singletons option) to identify singletons in my vcf file. I want to know what is the difference between singletons and doubletons. I am very confused after what I read in the VCFtools manual that the: > --singletons option will generate a file detailing the locatio ...
snp population genetics written 3 days ago by haneenih710
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Tess3r package, Barplots: How to have a specific color for each cluster and assign a new color to the new cluster when plotting higher K
... Hello, I obtained the ancestry matrix from sNMF and after that, I plot the bar plots (K2 to K4) using tess3r package as the following code line: my.colors =c("green","yellow", "red","blue") my.palette <- CreatePalette(my.colors, 9) ## barplot(qq, border = NA, pace = 0, x ...
R population genetics written 20 days ago by haneenih710
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Comment: C: How to sort the Q matrix from structure analyses based on countires first and th
... I don't have the q value in my data frame. However, I can calculate the q value and use the code line to sort. Thank you very much! ...
written 23 days ago by haneenih710
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How to sort the Q matrix from structure analyses based on countires first and then within the countires sort by q value
... Hi all, I am using tess3r package to plot bar plots of the Q matrix of ancestry coefficients that I got from sNMF analysis. But I am interested to order the matrix based on counties first and then based on Q, in another word, I want to have the matrix ordered by countires and within the conuty ord ...
R population genetics written 23 days ago by haneenih710
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Comment: C: How to find matching strings from two files, and if they match take the whole li
... This is pretty close. But doesn't give what I need. Maybe my explanation wasn't clear. However, my friend suggested this simple R code, that gave me what I want all <- read.table("file3.txt", stringsAsFactors = FALSE, header=T) a <- read.table("file1.txt", stringsAsFactors = FALSE,h ...
written 24 days ago by haneenih710
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How to find matching strings from two files, and if they match take the whole line/row in R
... Hello all, I have never used for loops and if statement in R, so I am struggling to solve my problem I have three files, two of them have 1 column that has genes IDs File #1 subgenA Dexi1A01G0002580.1 Dexi1A01G0002590.1 Dexi1A01G0002600.1 Dexi1A01G0012800.1 Dexi1A01G0002 ...
R written 26 days ago by haneenih710 • updated 26 days ago by Brice Sarver2.8k
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Comment: C: Masters in Bioinformatics
... check KAUST university. They give full scholarships. https://www.kaust.edu.sa/en ...
written 28 days ago by haneenih710
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Is it possible to find synteny between two subgenomes using a subset of annotation file
... Hello, I am interested to look at regions that experienced selective sweep in both subgenomes. I have identified a set of regions that are under selection in both subgenomes Example, identified regions from subgenome A Dexi_CM05836_chr04A maker gene 10734723 10737376 . + . ID=Dexi4A01G001273 ...
gene genomics written 28 days ago by haneenih710
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Comment: C: How can I confirm that detection of selective sweep is not by chance?
... What I meant is that you can't find a single gene under selection. because as I said for example MYB gene was found in the peak (meaning that it's under selection), but MYB gene is also present somewhere else in the genome. So MYB gene might be present in the peak just by chance ...
written 28 days ago by haneenih710
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Answer: A: Detection of selection by calculating nucleotide diversity ratio (pi) pi wild/pi
... Perfect! Thank you very much for the explanation =) ...
written 4 weeks ago by haneenih710

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