How to use UPORA to annotate peak

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UROPA is a command-line tool that annotates genomic regions, where genomic regions are required to be in BED format, such as peak intervals generated by data such as chip,ATAC_seq. At the same time, it is necessary to provide a genome annotation information in GTF format, such as a reference genome file downloaded from a database such as UCSC,ensemble,ncbi. In the annotation results, we not only give the location of peak in the genome, but also give more comprehensive annotation information, such as the corresponding positive and negative chains, distance from genes, corresponding gene types and so on. The website of the official document is as follows

Https://uropa-manual.readthedocs.io/introduction.html

According to the relative position between the center of peak and the gene, the software divides the genome location of peak into the following types, as shown below.

Various installation methods are provided. Here I use to pull the official docker image directly. The usage is as follows.

Docker pull loosolab/uropa

The software requires three input files:

Comment file in GTF format

Peak file in BED format

Configuration file in JSON format

Usage is also relatively simple, I use the official test data, the steps are as follows

1. Download the genome annotation file wget ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh47.75.gtf.gz in GTF format

Gunzip Homo_sapiens.GRCh47.75.gtf.gz2. Download the peak interval file wget https://www.encodeproject.org/files/ENCFF966LMJ/@@download/ENCFF966LMJ.bed.gz in bed format

Gunzip ENCFF966LMJ.bed.gz3. Prepare the configuration file in JSON format

The configuration file is as follows

{

"queries": [

{"feature": "gene", "distance": 5000, "feature.anchor": "start", "show.attributes": "gene_name"}

{"feature": "gene", "distance": 5000, "feature.anchor": "center"}]

"priority": "False"

"gtf": "/ home/soft/uropa/Homo_sapiens.GRCh47.75.gtf"

"bed": "/ home/soft/research/uropa/ENCFF966LMJ.bed"

}

The configuration file is named config.json and the code is as follows

Docker run\

-- rm\

-v / home:/home\

Loosolab/uropa\

Uropa\

-I / home/soft/uropa/config.json

\-p / home/soft/uropa/uropa

The-I parameter specifies the path to the configuration file, and-p specifies the prefix for the output file. The output file is as follows

├── uropa_allhits.txt

├── uropa_besthits.txt

└── uropa_finalhits.txt

The contents of the three files are the same, but the number of lines is different, and the contents are as follows

The software will automatically give each peak an id, you can visually see the relationship between peak and genes, for more usage and details, please refer to the official documentation.

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