Installing Bismark on Ubuntu
Bismark is a bioinformatics tool to map bisulfite treated sequencing reads to a genome . It also determines cytosine methylation sites. In this article, we will install Bismark on Ubuntu.
Preparing the system
Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:
$ sudo apt-get update
$ sudo apt-get upgrade
To install Bismark, you need to download and install two other software: Bowtie2 and Samtools. So, let’s install them first as shown below.
$ sudo apt-get install -y bowtie2
Change to a directory where you want to download the software, let’s say, Downloads. Now, download Samtools using the following command:
$ cd Downloads/
$ wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
Extract the file and install using the following commands:
$ tar xjf samtools-1.10.tar.bz2
$ cd samtools-1.10/
$ sudo make install
Now check it by typing
$ samtools in the terminal. After successful installation, it should display its usage.
Now let’s move to the installation of the Bismark package.
Now, let’s move back to the Downloads directory and download the Bismark software.
$ cd ../
$ wget https://github.com/FelixKrueger/Bismark/archive/master.zip
Now, unzip the file.
$ unzip master.zip
It will create a new directory in Downloads, namely, Bismark-master. It contains all the executable files. You can also check the installation by typing
$ bismark, it should display the usage.
That’s all for the installation of Bismark on Ubuntu.
- Krueger, F., & Andrews, S. R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. bioinformatics, 27(11), 1571-1572.
[Tutorial] Trailing of paired end reads using Trimmomatic tool in GALAXY.
Trimmomatic is a read trimming tool for Illumina NGS data . It is a flexible tool providing several functions to be operated on reads. These functions include trailing, leading, and several other quality control operations. In this article, we are going to perform trailing on NGS paired-end reads data using the GALAXY platform . (more…)
How to extract methylation call using Bismark?
Bismark is bioinformatics to map bisulfite treated sequencing reads and to perform methylation calls . In this article, we are going to extract methylation information from Bismark alignment outputs. (more…)
Installing PANDAseq on Ubuntu
PANDAseq is a bioinformatics tool that aligns paired-ends of Illumina sequences . In this article, we are going to install PANDAseq on Ubuntu. (more…)
FiNGS- A New Software providing Filters for Next Generation Sequencing
We use somatic variant callers to detect mutations in cancer samples by comparing sequencing data tumor and normal sample pairs. This is followed by some ad-hoc filtering that may produce low precision data resulting in a large number of false positives. (more…)
IonCRAM: New Tool for Ion Torrent Sequence Files Compression
One of the major next-generation sequencing (NGS) technologies that are most frequently used in medical research is Ion Torrent. Software for Ion Torrent machines provides output in BAM files that are huge in size. Additionally, their compression is also space expensive. (more…)
Assembly of high-throughput mRNA-Seq data: A review
Transcriptome represents the complete set of all expressed transcripts (RNA molecules) present in a cell or tissue at a given point of time. The transcriptome is always dynamic in nature and keeps on changing with time driven by the external and internal environment. (more…)
Predictive metagenomics profiling: why, what and how ?
What is predictive metagenomics profiling?
Recently, predictive metagenomics profiling (PMP) has been added to the microbial ecologist’s arsenal of strategies for probing microbial communities. (more…)
High throughput sequencing has revolutionized the new world of bioinformatics research. Since everyone is aware of the Human Genome project in which the human genome has been sequenced, millions of species have been sequenced so far. Sequencing is a very important aspect of bioinformatics so new faster and better sequencing techniques are needed . New sequencing platforms produce biological sequence fragments faster and cheaper.
You must be logged in to post a comment Login