RNA-Seq Blog Transcriptome Research & Industry News
The occurrence of chimeric transcripts has been reported in many cancer cells and seen as potential biomarkers and therapeutic targets. Modern high-throughput sequencing technologies offer a way to investigate individual chimeric transcripts and the systematic information of associated gene expressions about underlying genome structural variations and genomic interactions. Both assembly-based and alignment-based methods are used for the investigation of chimeric transcripts.
The basic workflow for the detection of chimeric transcripts
The expression of transcripts in a cell is dynamic. Next-generation sequencing is rapidly becoming the method of choice for the exploration of gene expressions. Furthermore, unlike hybridization-based detection, RNA -Seq allows genome-wide analysis of transcription at single-nucleotide resolution, including identification of including alternative splicing sites, posttranscriptional modifications, and fusion genes. As of 2015, the three most widely used NGS platforms for RNA-Seq are SOLiD and Ion Torrent and Illumina. Most of the RNA-Seq experiments use Illumina paired-end sequencing that allows users to sequence both ends of a fragment and generate high-fidelity reads. For the reason, most of published methods majorly deal with Illumina RNA-Seq data for finding chimeric transcript.
Fusion finding and de novo assembly programs for RNA -Seq analysis
|
Name |
Source |
References |
|---|---|---|
|
Fusion finding algorithms |
||
|
BreakDancer |
Fan et al. [15] |
|
|
FusionSeq |
http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ |
Sboner et al. [16] |
|
MapSplice |
Wang et al. [17] |
|
|
Tophat-fusion |
http://ccb.jhu.edu.ezproxyhost.library.tmc.edu/software/tophat/fusion_ index.html |
Kim et al. [10] |
|
deFuse |
McPherson et al. [18] |
|
|
FusionHunter |
Li et al. [19] |
|
|
SnowShoes-FTD |
http://bioinformaticstools.mayo.edu/research/snowshoes-ftd/ |
Yan et al. [20] |
|
ChimeraScan |
Iyer et al. [21] |
|
|
FusionMap |
http://www.arrayserver.com/wiki/index.php?title=FusionMap |
Ge et al. [14] |
|
FusionFinder |
http://bioinformatics .childhealthresearch.org.au/software/fusionfinder/ |
Francis et al. [22] |
|
FusionAnalyser |
Piazza et al. [23] |
|
|
SAOPfusion |
Wu et al. [24] |
|
|
SAOPfuse |
Jia et al. [25] |
|
|
FusionCatcher |
Nicorici et al. [13] |
|
|
ViralFusionSeq |
Li et al. [26] |
|
|
PRADA |
Torres-Garcia et al. [27] |
|
|
Chimera |
http:///bioconductor.org/packages/release/bioc/html/chimera. html |
Beccuti et al. [28] |
|
TRUP |
Fernandez et al. [29] |
|
|
De novo assembly algorithms |
||
|
EBARDenovo |
Chu et al. [8] |
|
|
Trinity |
Grabherr et al. [30] |
|
|
Trans-ABySS |
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss |
Robertson et al. [31] |
|
Oases |
Schulz et al. [32] |
|
