User: rimgubaev

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rimgubaev70
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Posts by rimgubaev

<prev • 22 results • page 1 of 3 • next >
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What does LnP(D) per clusters K plot means?
... Hello everyone! I am new to GWAS analysis and currently read some papers related to it. I saw such a plot (LnP(D) per clusters K) in one paper and did not understand actually what it stands for. ![enter image description here][1] [1]: https://i.pinimg.com/originals/f7/50/5f/f7505f7f96341535045c5 ...
gwas population genetics written 18 days ago by rimgubaev70
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(Closed) How to remove the nucleotide sequences that correspond to Illumina adapters?
... How to remove the nucleotide sequence that correspond to adapters without removing the whole read? ![enter image description here][1] [1]: https://i.pinimg.com/originals/0f/b0/c9/0fb0c97e19a1f5c49c9505a6b3ec211c.png ...
read filtering adapter sequencing written 10 weeks ago by rimgubaev70 • updated 10 weeks ago by ATpoint13k
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(Closed) How to name the line at ggplot?
... Hi, Everyone! I want to annotate each line with factor variable (chain.lenght) like shown on the picture.![enter image description here][1] Is it possible? Here is my code: ggplot(mz_rt, aes(rt, mz, size = acex, colour = as.factor(double.bonds))) + geom_line(aes(group = as.factor(ch ...
ggplot written 3 months ago by rimgubaev70
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(Closed) What is the definition for FASTA?
... Hello everyone! I wonder if somebody explain why FASTA format is called FASTA and what is the short history of it? ...
fasta written 3 months ago by rimgubaev70
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Is it possible to make a PCA plot for samples using TPM exprssion values in R?
... I have a table with TPM expression values for several samples (10-12) and I want to create PCA plot in order to estimate similarity of raplicates of a certain conditions. If it possible could you please suggest some pipelines or commands for R? ...
pca tpm rna-seq written 5 months ago by rimgubaev70 • updated 5 months ago by andrew.j.skelton735.5k
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(Closed) Why plant biologists do not explain chosen concentrations of phytohormones used for plant treatment?
... It's not quite a bioinformatics question. Maybe you would suggest some other forum. And if you already faced this problem I would be grateful if you suggest some experimental papers where various concentration of phytohormones (Jasmonic and Salicylic acids are be preferable) have been applied and th ...
phytohormones concentrations written 5 months ago by rimgubaev70
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Why volcano plot has no points in the middle of plot?
... Here is an example of volcano plot produced using edgeR results on DEG analysis. So my question is why there is no values in the middle of plot (indicated by red circle)? ![Volcano plot][1] [1]: https://i.pinimg.com/originals/07/69/3d/07693dfcb3c8fe55fcae39d7caa64239.jpg ...
rna-seq volcano plot written 5 months ago by rimgubaev70 • updated 5 months ago by WouterDeCoster36k
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Comment: C: What is wrong with NCBI's gff file?
... Now it's clear, thanks! ...
written 6 months ago by rimgubaev70
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What is wrong with NCBI's gff file?
... This is a part of gff file for *Nicotiana tabacum* (tobacco) genome fasta. I must say that the fact that mRNA, gene, 1st exon and 1st CDS start at the same location (2309) is quite confusing! Any ideas? NW_015787321.1 Gnomon gene 2309 5631 . + . ID=gene43;Dbxref=GeneID:107775605;Name=LOC10777 ...
gff written 6 months ago by rimgubaev70
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Answer: A: Are there some ways to extract information in tabular format from text with regu
... Solved this problem! I've written a small python scrip which generates tab-formatted text using Nsite output. Here is the code: import sys import re a = sys.argv[1] # reading of input filename (first argument) b = sys.argv[2] # reading of output filename (second argument) ...
written 6 months ago by rimgubaev70

Latest awards to rimgubaev

Scholar 6 months ago, created an answer that has been accepted. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Scholar 6 months ago, created an answer that has been accepted. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?

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