User: rimgubaev
rimgubaev • 70
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Posts by rimgubaev
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7
votes
1
answer
123
views
7 follow
1
answer
... 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? ...
written 12 days ago by
rimgubaev • 70
• updated
12 days ago by
andrew.j.skelton73 ♦ 5.3k
0
votes
0
answers
34
views
0
answers
... 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 ...
written 18 days ago by
rimgubaev • 70
9
votes
2
answers
163
views
2
answers
... 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 ...
written 20 days ago by
rimgubaev • 70
• updated
20 days ago by
WouterDeCoster ♦ 32k
0
votes
1
answer
158
views
1
answers
... Now it's clear, thanks! ...
written 6 weeks ago by
rimgubaev • 70
7
votes
1
answer
158
views
1
answer
... 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 ...
written 6 weeks ago by
rimgubaev • 70
3
votes
2
answers
146
views
2
answers
... 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 weeks ago by
rimgubaev • 70
4
votes
2
answers
510
views
2
answers
... 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 10 weeks ago by
rimgubaev • 70
3
votes
2
answers
146
views
2
answers
... 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: ...
written 12 weeks ago by
rimgubaev • 70
0
votes
2
answers
207
views
2
answers
... Nice one but there are only KEGG maps. ...
written 12 weeks ago by
rimgubaev • 70
0
votes
0
answers
122
views
0
answers
... I am interested in regulatory elements that may affect gene expression under certain condition. For example the presence of several ABREs (Abscisic acid responsive elements) within promoter region indicate that this gene is likely to be up-regulated under unfavorable conditions or ABA treatment. In ...
written 12 weeks ago by
rimgubaev • 70
Latest awards to rimgubaev
Scholar
6 weeks 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 weeks 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
7 weeks 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
10 weeks 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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