Question: Detection of fusion events of Retrotransposons and genes/lncRNA from RNA-seq data using available tools ?
gravatar for Manvendra Singh
4.7 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

Hii All,

I am trying to get fusions of Endogenous Retroviral elements (ERVs) and genes/lncRNA. There are some nice tools out there work quite nicely for gene-gene fusions e.g. fusioncatcher etc.

I am searching something which could work well for ERVs and genes,

I already did something by my own, manipulating outputs from some tools, but there was quite low overlap and moreover results were inconsistent among replicates.

e.g. MapSplice2

I would appreciate if you can please advice me anything on this.

PS: If I can analyze outputs from TopHat2-fusion or STAR outputs in someway where I get more and significant fusions.





ADD COMMENTlink written 4.7 years ago by Manvendra Singh2.1k

I started recently working on fusions.I have been using STAR-fusion and it seems to provide good results,as in confirming the fusions which have a strong evidence of having a fusion related to a specific gene. I use a cut-off of Junction reads and spanning pairs both to get a significant support.

ADD REPLYlink written 3.4 years ago by Ron990

Hi Ron - what cutoffs do you use for Junction reads and Spanning fragments? Is it referenced anywhere?

ADD REPLYlink written 2.7 years ago by komal.rathi3.5k

Usually I use Junction Reads > 2 and Spanning Pairs > 1 for fusions with good support. Although there could be novel fusions with only Junction Reads or only Spanning Pairs .

ADD REPLYlink written 2.7 years ago by Ron990
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