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UROBORUS Documentation

Documentation for UROBORUS software

http://uroborus.openbioinformatics.org/

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UROBORUS Documentation | uroborus.openbioinformatics.org Reviews
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Documentation for UROBORUS software
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1 uroborus documentation
2 introduction
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5 example
6 prerequisites
7 output file format
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10 docs
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UROBORUS Documentation | uroborus.openbioinformatics.org Reviews

https://uroborus.openbioinformatics.org

Documentation for UROBORUS software

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Download - UROBORUS Documentation

http://uroborus.openbioinformatics.org/en/latest/download

The latest version (v0.1.3) can be downloaded from here. Users can download the cutting edge version from GitHub by. Git clone git@github.com:WGLab/uroborus.git. Several example files are provided below to help users test the software:. The alignment index file (-index): BowtieIndex files (Homo sapiens, hg19 version)can be downloaded from http:/ ccb.jhu.edu/software/tophat/igenomes.shtml. The genome annotation file (-gtf): gtf file. The genome sequence file (-fasta): fasta file. Provided by Read the Docs.

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The circular RNA world: July 2016

http://circrna.blogspot.com/2016_07_01_archive.html

The circular RNA world. Latest in research from the circRNA world. Monday, 18 July 2016. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Yu-Chen Liu and colleagues at the Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan has created a unique web resource CircNet. Creation of this resource systematically utilized transcriptome sequencing data sets to identify the expression of circRNAs in 464 RNA-seq samples. Links to this post.

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The circular RNA world: UROBORUS - New pipeline for Circular RNA detection from RNAseq data

http://circrna.blogspot.com/2016/07/uroborus-new-pipeline-for-circular-rna.html

The circular RNA world. Latest in research from the circRNA world. Saturday, 16 July 2016. UROBORUS - New pipeline for Circular RNA detection from RNAseq data. Song and and colleagues from the University of Southern California published a new circular RNA prediction algorithm. Song et al,. Nucl Acids Res. (2016) doi: 10.1093/nar/gkw075. First published online: February 11, 2016. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Comparison of circular RNA prediction tools.

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The circular RNA world: Software

http://circrna.blogspot.com/p/software.html

The circular RNA world. Latest in research from the circRNA world. Software for circular RNA Prediction. A software pipeline for finding circular RNAs from RNA-seq data, based on STAR. circRNA finder has the capacity to identify circRNAs with very proximal splice sites (below 100 bp). Https:/ github.com/orzechoj/circRNA finder. Python code to detect head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data. Https:/ github.com/marvin-jens/find circ. Hansen ...

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UROBORUS Documentation

UROBORUS is a computational pipeline to detect circular RNA from RNA-Seq data, based on junction reads from back spliced exons. Before using UROBORUS.pl, you should use TopHat to align the reads to genome, and get the unmapped.sam file. If the genome sequence in each chromosome (chr1.fa, chr2.fa, chr3.fa)is saved in the directory. The path for genome sequence should be set as. The following three software should be installed in your cluster or computer before running the UROBORUS.pl. Tophat -p 6 -o RL 9 ...

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