RNA-Seq: TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

[Newsbot!]

Syndicated from PubMed RSS Feeds

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Genome Biol. 2011 Aug 11;12(8):R72

Authors: Kim D, Salzberg SL

ABSTRACT: TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/.

PMID: 21835007 [PubMed - as supplied by publisher]



More...

[bharati]

Confusion between Spanning reads and spanning mate pairs

Can anybody please explain the difference between Spanning Reads and Spanning Mate pairs. As much I could understand Spanning reads are those reads which do not harbor the fusion point but Split reads do harbor it, but Spanning mate pairs are those spanning reads which are supported by their mate pairs and the number of Spanning mate pairs should be lesser than spanning reads, but this is not the case in my results.

[Charitra]

can anybody give me guidance on how to select fusion candidate after tophat2-fusion result.html for validation ?

[jp.]

Finally, I got the answer

[bharati]

Can u pls explain the ans u got.

[jp.]

1. check the location and significance of geens
2. high spanning read
3. PCR validation