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This article shows you how to achieve fusion gene operation in fusioncatcher, the content is concise and easy to understand, it will definitely brighten your eyes. I hope you can get something through the detailed introduction of this article.

1. Prepare for reference genome

Fusioncatcher also provides a script to prepare the reference genome, which automatically downloads data from websites such as Ensembl, so you need to connect to the Internet when using it, as follows

Fusioncatcher-build-g mus_musculus-o / db/mouse-w asia.ensembl.org

The-g parameter specifies the species name of the reference genome, the-o specifies the directory of the output, and the-w parameter specifies ensembl web service, the URL of the biomart. It should be noted that the-w parameter must be set to the same as in the above example, the default parameter is not allowed, and for humans and mice, because the file is downloaded from the gencode database, and the FTP address of gencode has changed, you have to manually modify the FTP address of gencode in the source code.

For the value of the-o parameter, you can refer to the following link

Ftp://ftp.ensembl.org/pub/current_fasta

Each species in this directory corresponds to a folder, and fusioncatcher downloads the sequence of the corresponding species according to the value of the-o parameter.

In addition to downloading files, this step also includes time-consuming steps such as indexing, so this step will take a long time to run, taking 5-10 hours.

For human, the official database is based on Ensembl release 90, which can be downloaded as follows

Mkdir-p / some/human/data/cd / some/human/data/wget http://sourceforge.net/projects/fusioncatcher/files/data/human_v90.tar.gz.aawget http://sourceforge.net/projects/fusioncatcher/files/data/human_v90.tar.gz.abwget http://sourceforge.net/projects/fusioncatcher/files/data/human_v90.tar.gz.acwget http://sourceforge.net/projects/fusioncatcher/files/data/human_v90.tar.gz.adcat human _ v90.tar.gz.* | tar xzln-s human_v90 current2. Running

The usage is as follows

Fusioncatcher\-d database_directory\-I fastq_directory\-o output_directory

The-d parameter specifies the directory of the reference genome of the species, the-I parameter specifies the directory of the original sequencing data fastq file corresponding to the sample, and the-o parameter specifies the directory of the output results.

For the directory where the original sequence is located, the results of multiple samples can exist at the same time, and the software will automatically identify the R1 and R2 data corresponding to different samples.

As fusioncatcher has a built-in quality control program, it will automatically remove adapter and low-quality analysis from fastq files, so we only need to provide the original sequencing data.

In the output directory, final-list_candidate-fusion-genes.txt is the final predicted fusion gene. There are many files in this directory, and the detailed explanation of each file can be found in the official documentation.

The above content is how to implement the fusion gene operation in fusioncatcher. Have you learned the knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

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