How to perform a rank normal transformation in R
In this tutorial, we will see how to perform a rank-based inverse normal transformation in R before a genome-wide association study (GWAS) or an expression quantitative trait loci (eQTL) analysis.…
How to perform a size factors normalization in R
In this article, we will see how to perform a size factors normalization in base R by reimplementing the DESeq2 function. What is a size factors normalization Before digging into…
How to create Manhattan plots in R
In this blog post, we will see how to make Manhattan plots in R with real data. Indeed, we will use the association statistics from an article that reports risk…
How to get the TSS of genes in R
Today, we will see how to get the transcription start site (TSS) of genes in R. Indeed, it is for example needed in expression quantitative trait loci (eQTL) analyses where…
How to prepare files from QTLtools for METAL
In this tutorial, we will see how to prepare nominal files from QTLtools for a meta-analysis using the METAL software. Columns from QTLtools On the one hand, here are some…
How to filter variants with a low MAF
To filter variants with a low minor allele frequency (MAF) from a variant call format (VCF) file, we can use softwares such as bcftools, plink or R. What is minor…
How to extract GT or DS fields from VCF files in R
In this guide, we will see how to extract genotype (GT) or dosage (DS) fields from VCF files in R. We will make a speed comparison between base R and…
How to perform a basic eQTL analysis in R
To perform a basic eQTL analysis in R, we will use the lm function from base R and extract the slope (also called beta, effect or estimate), the standard error,…
How to liftover genomic positions in R
To show you how to liftover genomic positions in R, we will use the association statistics from an article that reports risk loci from genome-wide association studies (GWAS) for one…
How to filter lowly expressed genes in R
Today, we will filter lowly expressed genes from RNA-seq datasets in R. This is an important step because genes must be expressed at a certain level to perform their biological…
My first annual blog traffic report
I've started this blog one year ago to help biologists learn bioinformatics. Now, I would like to share with you this first annual blog traffic report! My objective was to…
How to perform modular arithmetic in R
Today, we will see how to compute a modulo, how to perform modular arithmetic and why it can be useful for some bioinformatics tasks in R. For example, it is…
Examples of for loops and if conditions in Bash
This week, we will see eleven examples of for loops and if conditions in Bash. All of them are commonly used in bioinformatics analyses. For loops Example 1 cells=( "neutrophils"…
How to trim adapters with cutadapt
In this tutorial, we will cover how to trim adapters such as the Nextera Transposase Sequence and the Illumina Universal Adapter with cutadapt. What are adapter sequences? After library preparation,…
How to see biological networks in Cytoscape
In this article, we will see how to use Cytoscape to visualize biological networks. A network is a set of nodes (such as people) connected by edges (such as friendship).…
How to rename samples in FastQC
Do you want to learn how to rename samples in FastQC? FastQC is a free software to perform quality control of reads in fastq format. Tool used In this post,…
How to save plots in base R and ggplot2 on an HPC
Do you wonder how to save plots in base R and ggplot2 on an HPC (High-Performance Computer)? I also searched the internet for that a few years ago! And as…
How to make all variants heterozygous in a VCF file
This week, we will see how to make all variants heterozygous in a VCF file. The purpose of this step is to use this file for an unbiased allele-specific read…
How to filter reads that overlap indels in a BAM file
Today, we will see how to filter reads in a BAM file that overlap indels defined in a VCF file using the samtools software. Tools used In this post, we…
STAR –waspOutputMode SAMtag vs WASP
This time, we will compare STAR --waspOutputMode SAMtag vs WASP. Both of them perform allele-specific read mapping. STAR STAR is a well-known free software that align reads to a reference…