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…
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 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 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…
STAR –quantMode GeneCounts vs HTSeq
In this post, we will compare STAR --quantMode GeneCounts vs HTSeq. Their goal is to perform gene quantification during or after read mapping, respectively. To achieve this, they need a…
Reference files for sequencing and genotyping data
In this post, we will see where to download some reference files that are required for the analysis of RNA sequencing and SNP genotyping data. Genome versions The current genome…
7 useful Linux commands in bioinformatics
This post compiles 7 useful Linux commands in bioinformatics with examples: cat, wc, du, grep, awk, sed, and find. However, I will not review pwd, mkdir, cd, ls, mv, rm,…
How to use a Linux terminal on Windows
There are several ways to use a Linux terminal on Windows, each one having its own pros and cons. Dual booting A dual booting is the installation of two operating…
How to connect to an HPC on Windows
In this blog post, we will see how to connect to an HPC (High Performance Computer) on Windows. During my studies, I used the Putty software to do that but…
Permutations and combinations in Bash
This article about the generation of permutations and combinations in Bash using iteration will be the last of the series. Indeed, I have already written this kind of post for…