Tag: RNA-Seq

G-Mo.R-Se 20110111 – Gene MOdeling using RNA-Seq

G-Mo.R-Se 20110111

:: DESCRIPTION

G-Mo.R-Se  (Gene Modelling using RNA-Seq) is a method aimed at using RNA-Seq short reads to build de novo gene models.First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models.

::DEVELOPER

France Denoeud, Jean-Marc Aury, CEA, DSV, Institut de Génomique, Genoscope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 G-Mo.R-Se

:: MORE INFORMATION

Citation

Genome Biol. 2008;9(12):R175. Epub 2008 Dec 16.
Annotating genomes with massive-scale RNA sequencing.
Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, Delledonne M, Morgante M, Valle G, Wincker P, Scarpelli C, Jaillon O, Artiguenave F.

FusionQ v.5 – Detection and Quantification of Chimerical RNAs from Paired-end RNA-seq

FusionQ v.5

:: DESCRIPTION

FusionQ is a novel fusion detection tool based on paired-end RNA-Seq data. This tool can detect gene fusions, construct the structures of chimerical transcripts, and estimate their abundances. This tool employs a new approach, “residual sequence extension”, which extends the short segments of the reads by aggregating their overlapping reads. A list of filters are proposed to control the false-positive rate.

::DEVELOPER

Center for Bioinformatics & Systems Biology, The Methodist Hospital Research Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • boost thread
  • R Package
  • Perl
  • Bowtie, Cufflinks
  • SAMtools

:: DOWNLOAD

 FusionQ

:: MORE INFORMATION

Citation

Liu C, Ma J, Chang C, Zhou X:
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.
BMC Bioinformatics 2013, 14:193 doi:10.1186/1471-2105-14-193

BRANCH 1.8.1 – boosting RNA-Seq Assemblies with Partial or related Genomic Sequences

BRANCH 1.8.1

:: DESCRIPTION

BRANCH is a software that extends de novo transfrags and identifies novel transfrags with DNA contigs or genes of close related species. BRANCH discovers novel exons first and then extends/joins fragmented de novo transfrags, so that the resulted transfrags are more complete.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

:: DOWNLOAD

  BRANCH

:: MORE INFORMATION

Citation

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
Ergude Bao, Tao Jiang and Thomas Girke (2013)
Bioinformatics (2013) 29 (10): 1250-1259.doi: 10.1093/bioinformatics/btt127

SplicingCompass 1.0.1 – Differential Splicing Detection using RNA-Seq data

SplicingCompass 1.0.1

:: DESCRIPTION

SplicingCompass predicts genes that are differentially spliced between two different conditions using RNA-seq data. The software is based on geometric angles between high dimensional read count vectors and is able to predict genes that undergo differential splicing from next generation RNA sequencing data.

::DEVELOPER

the Network Modeling group (Moritz Aschoff, Rainer König) and the HUSAR Bioinformatics Lab(Agnes Hotz-Wagenblatt, Karl-Heinz Glatting)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

 SplicingCompass

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1141-8. doi: 10.1093/bioinformatics/btt101. Epub 2013 Feb 28.
SplicingCompass: differential splicing detection using RNA-seq data.
Aschoff M, Hotz-Wagenblatt A, Glatting KH, Fischer M, Eils R, König R.

ASprofile – Extracting, Quantifying and Comparing Alternative Splicing (AS) Events from RNA-seq data

ASprofile

:: DESCRIPTION

ASprofile is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASprofile

:: MORE INFORMATION

NSMAP 0.1.0 – Spliced Isoforms Identification and Quantification from RNA-Seq

NSMAP 0.1.0

:: DESCRIPTION

NSMAP (Nonnegativity and Sparsity constrained Maximum A Posteriori ) is designed to identify and quantify isoforms from RNA-seq by incorporating a sparsity term into expression level estimation to enable isoform structure prediction and expression estimation simultaneously.

::DEVELOPER

Center for Bioinformatics & Systems Biology, The Methodist Hospital Research Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NSMAP

:: MORE INFORMATION

Citation

Zheng Xia, Jianguo Wen, Chung-Che Chang, and Xiaobo Zhou,
“NSMAP: A Method for Spliced Isoforms Identification and Quantification from RNA-Seq
BMC Bioinformatics 2011, 12:162

rpkmforgenes.py – Calculating Gene Expression for RNA-Seq data

rpkmforgenes.py

:: DESCRIPTION

The python script rpkmforgenes.py is written for calculating gene expression for RNA-Seq data.

::DEVELOPER

Sandberg Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 rpkmforgenes.py

:: MORE INFORMATION

Citation

Ramsköld D, Wang ET, Burge CB, Sandberg R (2009)
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data.
PLoS Comput Biol 5(12): e1000598. doi:10.1371/journal.pcbi.1000598

BEERS – Benchmarker for Evaluating the Effectiveness of RNA-Seq Software

BEERS

:: DESCRIPTION

BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data

::DEVELOPER

the Computational Biology and Informatics Laboratory (in the Center for Bioinformatics at the University of Pennsylvania)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 BEERS

:: MORE INFORMATION

Citation:

Gregory R. Grant, Michael H. Farkas, Angel Pizarro, Nicholas Lahens, Jonathan Schug, Brian Brunk, Christian J. Stoeckert Jr, John B. Hogenesch and Eric A. Pierce.
Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM) 
Bioinformatics. 2011 Sep 15;27(18):2518-28. Epub 2011 Jul 19.

RNAmapper v1 – Use of RNA-Seq data to Map and Identify Mutations in Zebrafish

RNAmapper v1

:: DESCRIPTION

RNAmapper uses RNA-seq data to identify both a region of the genome linked to a mutation as well as candidate mutations that may be causal for the phenotype of interest. We have shown that the method can identify mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Here you will find information on how to map your mutations using RNA-Seq data.

::DEVELOPER

Adam Miller, Arish Shah, and Cecilia Moens

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX /Linux
  • R package / Galaxy

:: DOWNLOAD

 RNAmapper

:: MORE INFORMATION