How to determine reference genome used for alignment in BAM file

If you want to specify the human genome reference run the following command

Does the BAM file contain all the necessary information to regenerate the original FASTQ files?

If you'd like to specify the human genome reference, run the following command:

Bash cheat sheet I

Here are the bash scripts you frequently use to accomplish your tasks.

Bash cheat sheet II

Here we present the continuation of Bash cheat sheet I, providing more advanced Bash commands.

Container

A container is a lightweight package of an operating system that allows users to install software and its dependencies in isolated environments (called ‘containers’), making it a single, portable, shareable, and reproducible package, like Apptainer/Singularity or Docker. Unlike virtual machines, containers are lightweight, fast, and typically run on a Linux-based system. They are often best suited for running one or two applications.

How drop specific columns

If you want to remove or keep specific columsn, you can cut command.

How remove duplicated lines

Using awk

Sometimes lines are duplicated in your text file. You can easily remove these duplicates using awk

How remove the dupclicated columns

Using awk

Sometimes columns are duplicated in your text file. You can easily remove these duplicates using awk

how redirect output to sed

If you want to redirect the out of command,

passwordless ssh

We often use SSH (Secure Shell) to remotely connect to servers via the terminal. If you’re tired of entering a password every time you log in, follow the steps below to enable passwordless login.