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Forum: Bioinformatics 05-09-2014, 08:05 AM
Replies: 0
Views: 2,037
Posted By narges
RNA-seq sample clustering using NMF package

I want to cluster RNA-seq samples (417 samples) using based on the expression levels of a group of selected genes using NMF method. Having a matrix (mat) of expression levels with sample names as...
Forum: RNA Sequencing 04-17-2014, 06:47 AM
Replies: 3
Views: 2,161
Posted By narges
Yes, I meant the biological oriented variance. ...

Yes, I meant the biological oriented variance.
Thanks!
Is it true that point "Px" in smooth curve is the mean of count values for gene gene x in the condition p? So, it forms the curve based on...
Forum: RNA Sequencing 04-17-2014, 05:14 AM
Replies: 3
Views: 2,161
Posted By narges
DESeq raw variance

Variance in DESeq is the sum of shot noise and raw variance. The raw variance is the smooth function of estimated read counts and experimental condition. In the corresponding paper, it is mentioned...
Forum: Bioinformatics 02-07-2014, 11:16 AM
Replies: 5
Views: 2,760
Posted By narges
Many thanks for the help.

Many thanks for the help.
Forum: Bioinformatics 02-07-2014, 08:34 AM
Replies: 5
Views: 2,760
Posted By narges
Yes, they are and I have seen the document. I...

Yes, they are and I have seen the document. I assumed it is not possible to "reconstruct the fastq files using samtools" but not other purposes like "samtools view ...".
But is there an alternative...
Forum: Bioinformatics 02-07-2014, 06:57 AM
Replies: 5
Views: 2,760
Posted By narges
Does HTSeq accepts BAM files from Mapsplice?

Hi,

I have BAM files from Mapsplice and I wanted to quantify the expression levels with HTSeq. But I received following error. Do you think it is regarding the aligner or what is the problem?
...
Forum: Bioinformatics 09-06-2013, 04:15 AM
Replies: 1
Views: 2,733
Posted By narges
Spike in dataset to compare DESeq vs cuffdiff

Hi all,

I wanted to ask if you have any idea to be fair as much as possible when comparing two RNA-seq analysis methods like DESeq and cuffdiff. I know one ideal option is using spikein datasets,...
Forum: Bioinformatics 07-04-2013, 05:27 AM
Replies: 0
Views: 2,369
Posted By narges
edgeR VS deseq normalization

Hi,

I intend to run RNA-seq analysis using DESeq package. But since I am working on TMM normalization method I wanted to run DESeq with TMM as well. I wanted to ask if it is enough if I pass the...
Forum: Bioinformatics 01-22-2013, 10:31 PM
Replies: 8
Views: 8,131
Posted By narges
Thank you but can I ask how does this function...

Thank you but can I ask how does this function calculate the gene length? Because my problem is that I do not know how to get the gene length to calculate the RPKM values. The gtf file I have used is...
Forum: Bioinformatics 01-15-2013, 07:11 AM
Replies: 8
Views: 8,131
Posted By narges
Get the RPKM value of the genes analyzed using DESeq or edgeR

Hi,

I have done analyzation over RNA seq data using edgeR and DESeq to find DE genes (BAM files -> HTSeq -> edgeR and DEseq).
For some comparisons I need to have the RPKM values related to each...
Forum: Bioinformatics 12-12-2012, 07:13 AM
Replies: 0
Views: 1,546
Posted By narges
samseq in samr fdr cutoff

Hi,

I wanted to ask about the parameter: fdr.output. I was supposed that it is a cut off for the FDR but te problem is that I have run this method twice with different fdr.output but there are...
Forum: Bioinformatics 12-01-2012, 03:53 PM
Replies: 3
Views: 3,400
Posted By narges
This is what he has asked : "Take at least 10...

This is what he has asked : "Take at least 10 gene promoters of the top hits....."
I also was thinking it can not be meaningful :(
Forum: Bioinformatics 12-01-2012, 05:24 AM
Replies: 3
Views: 3,400
Posted By narges
finding promoters using ensembl biomart

Hi,

I have found the upstream promoter of length 200 for some genes using Ensembl Biomart. But my supervisor asked me to find 10 promoter of each gene and to find any similarity between them. How...
Forum: Bioinformatics 11-05-2012, 08:54 AM
Replies: 12
Views: 5,922
Posted By narges
I wanted to ask what do you mean by "All valid...

I wanted to ask what do you mean by "All valid alignments"? For example if I use "accepted_hits.bam" file from TopHat output, would it be acceptable? Because I have used this file as the BitSeq input...
Forum: Bioinformatics 11-05-2012, 05:04 AM
Replies: 1
Views: 1,490
Posted By narges
BitSeq input data

Hi,
I wanted to know what kind of input data I can use running BitSeq. I have the fastq files of the experiment plus the accepted hits bam file from TopHat. Are these files the acceptable input...
Forum: Bioinformatics 11-02-2012, 02:08 AM
Replies: 0
Views: 1,673
Posted By narges
SAMseq

Hi all,
The SAMseq output produces down and up regulated genes separately listed.
If I want to retrieve the first 1000 DE genes regardless the idea of up or down regulated, which property do you...
Forum: RNA Sequencing 10-28-2012, 07:44 AM
Replies: 0
Views: 1,242
Posted By narges
HTSEQ results format when using refseq hg19

Hi,
I think I am not familiar with gene id representations so I am confused about the results I found in read count file resulting from HTSEQ.
In order to obtain the file refseq hg19 has been used...
Forum: Bioinformatics 10-11-2012, 04:55 AM
Replies: 0
Views: 852
Posted By narges
retrieving NCBI hg19 gene length

Hi,
I have a file containing gene names (23400 names) in NCBI hg19 format and this file is obtained from RNA seq analysis using tophat and then HTSEQ. So this file contains the gene names and their...
Forum: Bioinformatics 10-08-2012, 01:58 AM
Replies: 0
Views: 998
Posted By narges
NOISeq installtaion error

Hi all,
I am trying to install NOISeq package from Bioconductor using commands : source("http://bioconductor.org/biocLite.R") biocLite("NOISeq")

but there is an error when installing: Warning...
Forum: Bioinformatics 09-16-2012, 05:04 AM
Replies: 4
Views: 1,849
Posted By narges
Yes the R packages are exactly what you...

Yes the R packages are exactly what you mentioned.
About the cufflinks version, first I used the latest version :2.0.2-beta
and I gained only 8 DE genes with pvalue <0.01. But then after reading...
Forum: Bioinformatics 09-16-2012, 03:20 AM
Replies: 0
Views: 1,459
Posted By narges
gene_exp.diff file from different versions of cuffdiff

Hi all,
Regarding my question I have found another threads but it could not help and I really need your help because my work deadline is approaching soon.
I have an rna-seq dataset (6 samples for...
Forum: Bioinformatics 09-16-2012, 01:17 AM
Replies: 4
Views: 1,849
Posted By narges
Dear dpryan, first thank you so much for your...

Dear dpryan, first thank you so much for your always useful answers.
Actually, I also have increased number of biological replicates up to 12 and still there is no significant differentially...
Forum: Bioinformatics 09-14-2012, 06:09 AM
Replies: 4
Views: 1,849
Posted By narges
quality value of fastq file and tophat

Hi all,
First forgive me if my question is trivial. I have an Illumina rna-seq dataset of two samples (the fastq files).
I have mapped them using tophat and the result of mapping so satisfactory,...
Forum: Bioinformatics 09-06-2012, 06:46 AM
Replies: 4
Views: 1,818
Posted By narges
Thank you so much, now it works

Thank you so much, now it works
Forum: Bioinformatics 09-06-2012, 06:02 AM
Replies: 4
Views: 1,818
Posted By narges
Thank you, but I have used the same command, I...

Thank you, but I have used the same command, I mean like this :

samtools view accepted_hits.bam | htseq-count - /hg19/Annotation/Genes/genes.gtf > count.txt

for the single end dataset which did...
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