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Search: Posts Made By: TiborNagy
Forum: Bioinformatics 02-09-2015, 04:03 AM
Replies: 4
Views: 2,257
Posted By TiborNagy
Try to run using one thread. More threads uses...

Try to run using one thread. More threads uses more memory.
Forum: Bioinformatics 02-05-2015, 12:22 AM
Replies: 1
Views: 706
Posted By TiborNagy
Try a dataset that is used in the reference...

Try a dataset that is used in the reference article.
Forum: Bioinformatics 02-05-2015, 12:10 AM
Replies: 2
Views: 1,014
Posted By TiborNagy
Gene Ontology is the answer for your question. ...

Gene Ontology is the answer for your question.
For example:
http://amigo.geneontology.org/amigo/search/ontology?q=heavy%20metal
Forum: RNA Sequencing 01-23-2015, 04:44 AM
Replies: 2
Views: 1,775
Posted By TiborNagy
Maybe your sample name is conflicted with the SQL...

Maybe your sample name is conflicted with the SQL syntax. Try to add another name for your sample.
Forum: Introductions 01-23-2015, 04:40 AM
Replies: 1
Views: 1,010
Posted By TiborNagy
For your second question: you need to map the...

For your second question: you need to map the reads back to the reference.
Forum: Bioinformatics 07-28-2014, 09:44 PM
Replies: 2
Views: 3,020
Posted By TiborNagy
I have found only this: ...

I have found only this:
http://www.ncbi.nlm.nih.gov/pubmed/16597239
Forum: Bioinformatics 07-28-2014, 09:37 PM
Replies: 1
Views: 989
Posted By TiborNagy
You need khi-square or Fisher exact test. For...

You need khi-square or Fisher exact test. For every SNP you have to create a 2x2 contingency table like this:
SNP in other strains SNP in other strains
...
Forum: Bioinformatics 07-28-2014, 09:24 PM
Replies: 2
Views: 1,364
Posted By TiborNagy
I think the dependencies are outdated. (lib.pm...

I think the dependencies are outdated. (lib.pm and Usage.pm)
Forum: Bioinformatics 07-28-2014, 09:16 PM
Replies: 4
Views: 5,311
Posted By TiborNagy
One problem that I can see in your script is...

One problem that I can see in your script is samples$condition. There is no such variable. Relevel works on DESeqDataSet.
Forum: Bioinformatics 07-25-2014, 05:45 AM
Replies: 2
Views: 790
Posted By TiborNagy
Hi sazz! Variance in gene expression is...

Hi sazz!

Variance in gene expression is not depends on FPKM. It is just a statistical measure of the replicates.

csmatyi:

I think you need khi-square test.
Forum: Bioinformatics 07-25-2014, 05:07 AM
Replies: 1
Views: 856
Posted By TiborNagy
No. I have checked the FTP sites and the SQL...

No. I have checked the FTP sites and the SQL tables. There is no loop sequence in miRBase. You can download hairpin sequences and use RNAfold on it.
Forum: Bioinformatics 07-07-2014, 04:47 AM
Replies: 4
Views: 2,662
Posted By TiborNagy
For GO enrichment analysis I have used Bingo from...

For GO enrichment analysis I have used Bingo from Cytoscape.
Forum: Bioinformatics 07-07-2014, 04:36 AM
Replies: 4
Views: 1,329
Posted By TiborNagy
I am learn a lot from Coursera...

I am learn a lot from Coursera (https://www.coursera.org/).
There is an article to help improving your skills:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002632
Forum: Bioinformatics 07-07-2014, 04:31 AM
Replies: 1
Views: 1,065
Posted By TiborNagy
Create a set from the accession numbers, read the...

Create a set from the accession numbers, read the two fasta file and store the headers as a set. Now you can use intersection() method to get common elements....
Forum: Bioinformatics 07-07-2014, 04:24 AM
Replies: 1
Views: 1,260
Posted By TiborNagy
For bacteria 25x coverage is good. Backbone is...

For bacteria 25x coverage is good.
Backbone is very important. Mira can handle SNP and short indels (4-5 nt length), but you won't see longer variations.
Forum: Bioinformatics 07-07-2014, 04:18 AM
Replies: 2
Views: 998
Posted By TiborNagy
This article: ...

This article:
http://www.nature.com/ncomms/2013/130806/ncomms3274/full/ncomms3274.html
contains the information where can you download the genome.
The transcriptome also available. You need to run...
Forum: Bioinformatics 07-07-2014, 04:09 AM
Replies: 4
Views: 1,340
Posted By TiborNagy
The documentation suggest you need to use a...

The documentation suggest you need to use a differential expression analysis solution: DESeq2, Cufflinks, Limma and after that use gage. These packages handle the replicates.
Forum: Bioinformatics 06-19-2014, 05:54 AM
Replies: 1
Views: 1,211
Posted By TiborNagy
Why do not use Blast? If the query and the...

Why do not use Blast? If the query and the database are the same, it will find all the duplicated regions.
Forum: Bioinformatics 06-19-2014, 05:48 AM
Replies: 2
Views: 2,078
Posted By TiborNagy
The frequency of every kmer should be a...

The frequency of every kmer should be a dimension. Than you can use PCA.
Forum: Bioinformatics 06-19-2014, 05:44 AM
Replies: 4
Views: 2,129
Posted By TiborNagy
The guide_tree file is a newick tree format,...

The guide_tree file is a newick tree format, every program could read this format.
I have used R:

library(ape)
t <- read.tree("mauve.out.guide_tree")
plot(t)
Forum: RNA Sequencing 06-19-2014, 05:37 AM
Replies: 2
Views: 1,801
Posted By TiborNagy
Use TopHat to align reads. This create a proper...

Use TopHat to align reads. This create a proper BAM file.
Forum: Bioinformatics 06-19-2014, 05:34 AM
Replies: 4
Views: 2,662
Posted By TiborNagy
Yes. Yes.

Yes.

Yes.
Forum: Bioinformatics 06-19-2014, 05:21 AM
Replies: 1
Views: 2,017
Posted By TiborNagy
A read can not be unique, if it has more than one...

A read can not be unique, if it has more than one equally good hits. The -n argument is just set the maximum number of alignments.
Forum: Bioinformatics 06-19-2014, 05:10 AM
Replies: 1
Views: 1,030
Posted By TiborNagy
As far as I know MEGA is not a parallel program....

As far as I know MEGA is not a parallel program. It's use only one cpu/core.
Forum: Bioinformatics 06-19-2014, 05:03 AM
Replies: 3
Views: 1,419
Posted By TiborNagy
First you need to create an annotation (RAST) and...

First you need to create an annotation (RAST) and after that you can use snpeff.
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