I just skimmed through this post a couple of days back. It seems to be a method to correct the bias in the RNA-Seq data without loss using conditional quantile normalization. Has anyone ever tried this? Or have some idea about this? Seems interesting.
Is it for differential gene expression? If so, there is also this group that is looking at bias due to gene length and sequencing depth : http://bioinfo.cipf.es/aconesa/research3.html
Their tool is called NOISeq
Hi. I am studying a protein that potentially affects H2A.Z levels by regulating the complex depositing this histone variant (SWR1c). So we did ChIP-seq in …
Hi everyone, first of all Iam a biologist so sorry for the (potentially) very basic question. We performed ATAC-seq (treatment vs. control in duplicates) and …
<p>Hi everyone,</p> <p>I've been stuck on this for several days. I want to use the <a href='http://samtools.sourceforge.net/'>samtools</a> depth command but not only for a single …
<p>Has anyone else ever randomly ran into the problem of misencoded quality scores with the GATK? This happened once before and now just recently again …
<p>Lately I came across several papers on this area: <a href="http://evfold.org/">http://evfold.org/</a> or psicov My question is that if anyone of you have actually used it …
<p>Hello all,</p> <p>From a <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> (or <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a>) file, by looking at the <code>MD:Z field</code>, we could identify the position of mismatches. For example, …
<p>Hello, Suppose I have RNA-seq data for 1) control, say, <code>T0</code> 2) treatment after 4 hours <code>T4</code> 3) treatment after 8 hours <code>T8</code> and I …
<p>Hi</p> <p>I am using R for a simple hierarchical clustering method for finding protein sequence similarities. I already have a distance matrix computed. I am …
<p>I am working on alternative splicing (AS) events on 4 different tomato species. I am trying to find <code>interesting</code> AS events.</p> <p>Lets say for example, …
There's also this: http://genomebiology.com/content/12/3/R22
Is it for differential gene expression? If so, there is also this group that is looking at bias due to gene length and sequencing depth : http://bioinfo.cipf.es/aconesa/research3.html Their tool is called NOISeq