User: Radek
Radek • 820
- Reputation:
- 820
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- Belgium
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- 10 hours ago
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- 1 year, 12 months ago
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Posts by Radek
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... Hi!
I am trying to use ***WTSI Mutational Signature Framework*** from Alexandrov L. to deconstruct some mutation patterns.
http://nl.mathworks.com/matlabcentral/fileexchange/38724-wtsi-mutational-signature-framework
Unfortunately I am not familiar at all with matlab. I got from my university a ve ...
written 8 days ago by
Radek • 820
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Comment:
C: RNA-Seq in Bioconductor
... Have you red the DESeq2 manual? It is full of examples at the end. Each of them can be downloaded through R. ...
written 12 days ago by
Radek • 820
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Comment:
C: R loop not functional
... I am not sure I understand what you want to do. Is it "if your value(gene X) is comprised between value(gene A) +/- 0.3 you print something like 'TRUE' if not 'FALSE' " ?
If so it would be either to go for a statement like the following one: if(b < a+0.3 | b > a-0.3) print(TRUE) else { print ...
written 13 days ago by
Radek • 820
3
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Answer:
C: RNA seq data analyses
... Have thought about using a differential expression analysis?
Using a program such as DESeq2/edgeR/Limma to compare your tissues with or without treatment ( ~ alcohol_treatment) and your cells with or without treatment ( ~ alcohol_treatment) separately. Then looking in those two analysis which gene ...
written 27 days ago by
Radek • 820
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... Do you mean finding genes or features which are differentially expressed between groups? The "measure independent variable to get unique values" is a bit confusing. ...
written 28 days ago by
Radek • 820
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109
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Comment:
C: Use blastn to predict miRNA
... For small rna use bowtie1. This usually gives me good results.
Sometimes simplier approaches are the best. If the results make sense and can be validated after your are in buisness. ...
written 28 days ago by
Radek • 820
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3
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109
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Comment:
C: Use blastn to predict miRNA
... Since you have HTS data you should have a look to these tools to find new miRNAs: https://omictools.com/ncrna-identification-category
and probably this publication: [https://www.ncbi.nlm.nih.gov/pubmed/23334922][1]
if you still want to try to blast your data I think your method is a good starting p ...
written 28 days ago by
Radek • 820
0
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3
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109
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Comment:
C: Use blastn to predict miRNA
... What is your starting input? (small RNA-seq fastq?) and what is exactly your goal? (find new miRNAs which are not highly conserved between your specie of interest and a database?) ...
written 28 days ago by
Radek • 820
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... There are indeed many different aligners. One of the simplest and fastest one is bwa (burrows wheeler aligner). Bowtie2 also used a lot.
There are many reviews in the litterature about those aligners. Give it a go, that's generally a good place to start.
NB: Most aligners do an excellent job on ev ...
written 5 weeks ago by
Radek • 820
2
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... It doesn't really tell us for what is it but here is a code in R to get the count data into a matrix:
- Assuming that this is in a text file (and not excel) that is located on your desktop at this address: "~/Desktop/count.txt"
a <- read.table("~/Desktop/count.txt", header=T, row.names=1, s ...
written 5 weeks ago by
Radek • 820
Latest awards to Radek
Teacher
26 days ago,
created an answer with at least 3 up-votes.
For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Commentator
5 weeks ago,
created a comment with at least 3 up-votes.
For C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For C: Is going back to the wet lab worth it?
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For C: Is going back to the wet lab worth it?
Appreciated
6 months ago,
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For C: Is going back to the wet lab worth it?
Teacher
6 months ago,
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question
9 months ago,
created a question with more than 1,000 views.
For DESeq2 analysis: huge number of outliers and refitting
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For MA plots DESeq: strange MA plots
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10 months ago,
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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14 months ago,
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For DESeq2 analysis: huge number of outliers and refitting
Student
24 months ago,
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For MA plots DESeq: strange MA plots
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