UROBORUS

UROBORUS

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UROBORUS is a computational pipeline to detect circular RNA supported by junction reads from back spliced exons.

Download the latest version of UROBORUS. Version: 0.0.2. Last Modified: 2016-3-06

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Authors: Xiaofeng Song (xfsong.nuaa@gmail.com or xfsong@nuaa.edu.cn)

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Usage:

Before using UROBORUS.pl, you should use TopHat to align the reads to genome, and get the unmapped.sam file.

UROBORUS.pl 0.0.2 #circRNA identification tool in total RNA-seq data

usage:

perl UROBORUS.pl -index /path/genome -gtf /path/genes.gtf -fasta /path unmapped.sam

Options:

-index: genome index (use bowtie1 index);

-gtf: gene annotation file (*.gtf file);

-fasta: path for genome sequence in fasta file (*.fa) in separate chromosome;

-p: threads (Integer, default = 6);

-temp: keeping the temporary file;

-help: usage help;

Note:

  • 1.If the genome sequence in each chromosome (chr1.fa, chr2.fa, chr3.fa, …)is saved in the directory /home/circRNA/Gene, the path for genome sequence should be set as “-fasta /home/circRNA/Gene”;
  • 2.The following files ( genome index, gene annotation, genome sequence) should be download from TopHat webstie: http://ccb.jhu.edu/software/tophat/igenomes.shtml
  • Example:

    perl UROBORUS.pl -index /home/***/index/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome -gtf /home/***/circRNA/Gene/genes.gtf -fasta /home/***/circRNA/Gene unmapped.sam

    Example files download:

  • 1. The alignment index file (-index): Bowtie1 index files (Homo_sapiens, hg19 version)can be downloaded from http://ccb.jhu.edu/software/tophat/igenomes.shtml
  • 2. The genome annotation file (-gtf): gtf file
  • 3. The genome sequence file (-fasta): fasta file
  • 4. Input file -- The unmapped SAM format file (rar file): unmapped sam file
  • 5. Output file -- The reported circRNA list : circRNA list file
  • The above first 3 files are from Homo_sapiens genome (hg19 version), other species genome files can be downloaded from http://ccb.jhu.edu/software/tophat/igenomes.shtml

    Software Prerequisites:

    The following three software should be installed in your cluster or computer before running the UROBORUS.pl

  • TopHat
  • tophat -p 6 -o RL_9_tophat_out /home/***/index/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome

    /home/***/data/Glioblastoma/RL_9_OLI_GTCCGC_L008_R1_001.fastq /home/***/data/Glioblastoma/RL_9_OLI_GTCCGC_L008_R2_001.fastq

  • samtools
  • Convert unmapped.bam to unmapped.sam (using samtools view)

    samtools view unmapped.bam > unmapped.sam

  • Bowtie1
  • Output file format:

    The first 3 columns are the same with bed file format.

    1. Chromosome

    2. start of junction

    3. end of junction

    4. strand

    5. Parental gene name

    6. genomic distance

    7. read counts

    8. matched transcript id

    Copyright (C) 2015 Xiaofeng Song.

    Reference:

    Xiaofeng Song, Naibo Zhang, Ping Han, Byoung-San Moon, Rose K. Lai, Kai Wang, Wange Lu. Circular RNA profile in gliomas revealed by identification tool UROBORUS. Nucleic Acids Research, 2016,1.doi: 10.1093/nar/gkw075. Full Text