Dear all
I am very new to this so apologies in advance..
I am trying to teach myself the basics of R and bioinformatics...
17 results in 0.0049 seconds.
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Normalisation of RNAseq data from UCSC Xena Browser
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Processing a very large soil dataset
I’ve been tasked with assembling a very large soil metagenomic dataset, so large that I’m having second thoughts about my regular processing pipeline,... -
Bio-statistics for metatranscriptomic
Hi everybody,
I am trying to identified differentially expressed (DE) genes of several bacterial metatranscriptomes.
To sum up... -
DiffBind read counts normalisations
Is there a way to turn off the normalisation by the library size (either full or effective) in DiffBind?
The problem is that I the bam... -
Left-normalisation of variants using R
I'm writing a mitochondrial haplotyping script in R, and one of the things I needed to do was left-normalisation of INDELs. Because of the way the variants... -
Normalization by the library size during variant detection
Hello:
Suppose I have two libraries that do not have the same number of reads, but otherwise they are similar. During variant detection,... -
Normalisation of small non coding RNA (miRNA and tRNA fragments)
Hello all,
I have been sequencing small non coding RNA using hiseq 100pb single paired
I then used mirdeep2 to... -
fold change for rna seq data without replicates
Hi all!
I have bacterial metatranscriptome from 12 samples but I don't have any biological replicates. They are a time serie (1 sample for each... -
zero rna-seq values AFTER normalisation in edgeR
I am using edgeR to analyze RNA-Seq data. This is my script:
library("edgeR")
#############################... -
Microarray normalisation for in-house made platform
Hello,
I am trying to do a microarray analysis on a time-series (5 time points) gene expression (GE) data of 3000 genes. I want to calculate... -
Equimolar pooling of hundreds of libraries for sequencing
Recently Ilumina released additional sets of barcoded Nextera primers which enable multiplexing 384 samples for sequencing. High level of multiplexing...Last edited by nucacidhunter; 05-08-2014, 06:24 AM. -
RNA-seq normalization: How to use TMM and rpkm() in EdgeR??
Hi,
I have some RNA-seq samples that I want to normalize and then output RPKM expression, but I am unsure how to do this.
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FPKM despite no length ~ count correlation?
Hi all,
I am working with Illumina HiSeq paired-end reads mapped with Bowtie2 to a bacterial reference genome in 3 biological replicates.... -
CuffLinksLibrary Normalization Methods: classic-fpkm vs -N/--upper-quartile-norm
According to the Cufflinks manual, the only option for library normalization is the "classic-fpkm" method. However, under Advanced Abundance... -
Nextera XT Normalisation
Hi all,
I have been using the Nextera XT kit to do my library preps for MiSeq sequencing of fairly low complexity libraries and have been...
