User: rimgubaev

gravatar for rimgubaev
rimgubaev70
Reputation:
70
Status:
Trusted
Location:
Last seen:
5 days, 15 hours ago
Joined:
9 months, 3 weeks ago
Email:
r********@gmail.com

Posts by rimgubaev

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
51
views
0
answers
(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 12 days ago by rimgubaev70
4
votes
0
answers
145
views
5 follow
0
answers
(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 17 days ago by rimgubaev70
10
votes
1
answer
218
views
7 follow
1
answer
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 9 weeks ago by rimgubaev70 • updated 9 weeks ago by andrew.j.skelton735.4k
0
votes
0
answers
64
views
0
answers
(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 10 weeks ago by rimgubaev70
9
votes
2
answers
241
views
2
answers
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 10 weeks ago by rimgubaev70 • updated 10 weeks ago by WouterDeCoster34k
0
votes
1
answer
221
views
1
answers
Comment: C: What is wrong with NCBI's gff file?
... Now it's clear, thanks! ...
written 3 months ago by rimgubaev70
7
votes
1
answer
221
views
1
answer
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 3 months ago by rimgubaev70
3
votes
2
answers
177
views
2
answers
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 3 months ago by rimgubaev70
4
votes
2
answers
605
views
2
answers
Answer: A: How to extract all promoter regions in multi-fasta format from genome using GFF?
... Finally, I've solved this problem by combining samtools, bedtools as well as custom R script. The pipline placed into bash script is available [here](https://github.com/RimGubaev/extract_promoters). ...
written 4 months ago by rimgubaev70
3
votes
2
answers
177
views
2
answers
Are there some ways to extract information in tabular format from text with regular pattern?
... Hello everyone! I have an output from [NsiteM](http://www.softberry.com/berry.phtml?topic=nsitem&group=programs&subgroup=promoter) which represents a text with promoter analysis results. The text has a regular pattern: 1. QUERY: Gene1 Length of Query Sequence: ...
nsitem promoter analysis text mining written 4 months ago by rimgubaev70

Latest awards to rimgubaev

Scholar 3 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 3 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 3 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 4 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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1323 users visited in the last hour