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How to extract methylation call using Bismark?

Dr. Muniba Faiza

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How to extract methylation call using Bismark?

Bismark is bioinformatics to map bisulfite treated sequencing reads and to perform methylation calls [1]. In this article, we are going to extract methylation information from Bismark alignment outputs.

1. Preparing genome (Indexing)

Let’s first prepare our genome as it should be bisulfite converted to proceed further. This step needs to be done only once.

$ bismark_genome_preparation [options] /path/to/genome/folder

Let’s assume your genome is present in Documents/genomes/homo_sapiens/.

If Bowtie2 is not in your path, then use the following command for genome preparation:

$ bismark_genome_preparation --path_to_aligner /usr/bin/bowtie2/ --verbose /Documents/genomes/homo_sapiens/GRCh38/

2. Alignment

In this step, we perform the actual bisulfite alignment. Here, you have to specify the directory containing the genome of interest in FASTA format and a single or multiple sequence files to be analyzed. These files must be in FastA or FastQ format.

$ bismark [options] --genome <genome_folder> {-1 <mates1> -2 <mates2> | <singles>}

For example, let’s say your sequence file is test_data.fastq and is present in the same directory, then the command will be as shown below:

$ bismark --genome /Documents/genomes/homo_sapiens/GRCh37/ test_data.fastq

This will produce two files as output:

  • test_data_bismark_bt2.bam – This file will contain all alignments and methylation call strings.
  • test_data_bismark_SE_report.txt –  This file will contain alignment and methylation summary.

3. Deduplication

This step is performed to deduplicate the Bismark alignment BAM file. It will remove all reads except the one aligned to the very same position.

$ deduplicate_bismark --bam [options] <filenames>

4. Methylation Extraction

This command will extract the context-dependent (CpG/CHG/CHH) methylation. Here, we will use the output file generated in step 2.

$ bismark_methylation_extractor [options] <filenames>

For example,

$ bismark_methylation_extractor --gzip --bedGraph test_data_bismark_bt2.bam

This command will generate three main output files and two other files:

  • CpG_context_test_dataset_bismark_bt2.txt.gz
  • CHG_context_test_dataset_bismark_bt2.txt.gz
  • CHH_context_test_dataset_bismark_bt2.txt.gz
  • A bedgraph, and
  • Bismark coverage file

The output files will show:

  • seq-ID
  • methylation state
  • chromosome
  • start position (end position)
  • methylation call

For more information on output, click here.


Reference

  1. Krueger, F., & Andrews, S. R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. bioinformatics27(11), 1571-1572.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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NGS

[Tutorial] Trailing of paired end reads using Trimmomatic tool in GALAXY.

Dr. Muniba Faiza

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How to generate config file for docking using Autodock Tools?

Trimmomatic is a read trimming tool for Illumina NGS data [1]. 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 [2]. (more…)

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NGS

Installing PANDAseq on Ubuntu

Dr. Muniba Faiza

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Installing pandaseq on Ubuntu

PANDAseq is a bioinformatics tool that aligns paired-ends of Illumina sequences [1]. In this article, we are going to install PANDAseq on Ubuntu. (more…)

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NGS

Installing Bismark on Ubuntu

Dr. Muniba Faiza

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Installing Bismark on Ubuntu

Bismark is a bioinformatics tool to map bisulfite treated sequencing reads to a genome [1]. It also determines cytosine methylation sites. In this article, we will install Bismark on Ubuntu. (more…)

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