Tag: Paired End RNA-Seq

comrad 0.1.3 – Discovery of Gene Fusions using Paired End RNA-Seq and WGSS

comrad 0.1.3

:: DESCRIPTION

Comrad is a novel algorithmic framework for the integrated analysis of RNA-Seq and Whole Genome Shotgun Sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 comrad

:: MORE INFORMATION

Citation

Andrew McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach1, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins and S. Cenk Sahinalp
Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data
Bioinformatics (2011)doi: 10.1093/bioinformatics/btr184

FusionHunter 1.4 – Identify Fusion Transcripts from Transcriptional Analysis of Paired-end RNA-seq

FusionHunter 1.4

:: DESCRIPTION

FusionHunter is a software which reliably identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset. The purpose of FusionHunter is to identify potential fusions with high sensitivity and specificity and to guide further functional validation in the laboratory.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FusionHunter

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1708-10. Epub 2011 May 5.
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
Li Y, Chien J, Smith DI, Ma J.