Hello, I want to do normalization for read count from the gtex portal. I was reading about gtex normalization for qtl analysis. The read count …

I am trying to impute SNP array data on the Michigan imputation server. My overlap with the reference panel is about 60%, but is leading …

Hello Everyone! I am working on GWAS and need to filter raw data (esp missing, maf, callrate). It has usually done in Tassel. However, is …

<p>What tool do you use for removing adapters and low-quality portions of reads and why?</p>

Hello, I'm using plink for QC. I have two questions re MAF: 1. My understanding is that plink (`plink --file data --freq`) will estimate the …

<p>Hey guys,</p> <p>I&#39;m currently working on my final project for college and it&#39;s about finding SNPs. So the basic idea is to implement a method …

<p>I have aligned my BS-Seq data with Bismark and I removed as well the duplicated fragments (I am following the commands from this <a href="http://www.bioinformatics.babraham.ac.uk/training/Methylation_Course/Basic%20BS-Seq%20processing%20practical.pdf">link</a>). …

<p>Hello,</p> <p>I&#39;m dealing with RNA-seq data. I have expression values in FPKM.</p> <p>Should I plot them as RPKM, or using `log2`? Why?</p> <p>Thanks.</p>

<p>Hello,</p> <p>I&#39;ve downloaded GO terms from Phytozome using Biomart. I&#39;d like to know what is the real source of those GO terms and the version …

<p>Hello guys,</p> <p>I am doing a project in RNA-seq data with some datasets that are paired-end data. After alignment with TopHat2, I have around 1-5% …