Forum: Bioinformatics
05-09-2014, 09:05 AM
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Replies: 0
Views: 2,179
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...
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Forum: RNA Sequencing
04-17-2014, 07:47 AM
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Replies: 3
Views: 2,294
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Forum: RNA Sequencing
04-17-2014, 06:14 AM
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Replies: 3
Views: 2,294
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...
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Forum: Bioinformatics
02-07-2014, 12:16 PM
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Replies: 5
Views: 3,064
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Forum: Bioinformatics
02-07-2014, 09:34 AM
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Replies: 5
Views: 3,064
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...
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Forum: Bioinformatics
02-07-2014, 07:57 AM
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Replies: 5
Views: 3,064
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?
...
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Forum: Bioinformatics
09-06-2013, 05:15 AM
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Replies: 1
Views: 2,835
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,...
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Forum: Bioinformatics
07-04-2013, 06:27 AM
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Replies: 0
Views: 2,475
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...
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Forum: Bioinformatics
01-22-2013, 11:31 PM
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Replies: 8
Views: 8,383
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...
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Forum: Bioinformatics
01-15-2013, 08:11 AM
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Replies: 8
Views: 8,383
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Forum: Bioinformatics
12-12-2012, 08:13 AM
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Replies: 0
Views: 1,622
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...
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Forum: Bioinformatics
12-01-2012, 04:53 PM
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Replies: 3
Views: 3,601
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Forum: Bioinformatics
12-01-2012, 06:24 AM
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Replies: 3
Views: 3,601
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...
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Forum: Bioinformatics
11-05-2012, 09:54 AM
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Replies: 12
Views: 6,090
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...
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Forum: Bioinformatics
11-05-2012, 06:04 AM
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Replies: 1
Views: 1,565
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...
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Forum: Bioinformatics
11-02-2012, 03:08 AM
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Replies: 0
Views: 1,750
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...
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Forum: RNA Sequencing
10-28-2012, 08:44 AM
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Replies: 0
Views: 1,342
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...
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Forum: Bioinformatics
10-11-2012, 05:55 AM
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Replies: 0
Views: 935
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...
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Forum: Bioinformatics
10-08-2012, 02:58 AM
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Replies: 0
Views: 1,050
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...
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Forum: Bioinformatics
09-16-2012, 06:04 AM
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Replies: 4
Views: 1,957
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...
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Forum: Bioinformatics
09-16-2012, 04:20 AM
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Replies: 0
Views: 1,549
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Forum: Bioinformatics
09-16-2012, 02:17 AM
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Replies: 4
Views: 1,957
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...
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Forum: Bioinformatics
09-14-2012, 07:09 AM
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Replies: 4
Views: 1,957
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,...
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Forum: Bioinformatics
09-06-2012, 07:46 AM
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Replies: 4
Views: 1,938
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Forum: Bioinformatics
09-06-2012, 07:02 AM
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Replies: 4
Views: 1,938
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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