How To Identify Large Arrangements And Transposable Elements In Ngs Data?

Question

[Jordan]

Hi,

I finished mapping and variant calling on these for solid data. Now I'm looking to identify large rearrangements and transposable elements. Can anyone tell me any good tools for these? One tool I have come across now is nFuse. I wanted to know what the general pipeline for this is.

And I would like to view such arrangements as Circos plots.

Thanks for the help.

[Biomonika (Noolean)]

Concerning identification of new transposable element insertions I recommend this paper: Landscape of somatic retrotransposition in human cancers. The idea is presented in figure 1: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656569/figure/F1/

Answer 1

[Casey Bergman]

There are a number of non-reference TE insertion mapping tools available now including:

• RelocaTE
• ngs_te_mapper
• PoPoolationTE
• TE-locate
• RetroSeq
• TEMP

These systems differ in how they map NGS reads, how they discover and represent non-reference TEs in a genome (see How Are Transposable Elements Represented In A Genome?), and in their final output file formats. We have tried to characterise the major features of each of these systems (besides TEMP) in this poster. There has been no systematic evaluation of all of these methods, so it is difficult to say which is the "best".

In the absence of a thorough evaluation study, our view is that it is necessary to run multiple TE mapping tools and evaluate the impact that different tools have on your biological conclusions. To this end, we are currently developing a meta-pipeline called McClintock that installs and runs all of the tools listed above (besides TEMP) and outputs results in a standard BED format.

Answer 2

[Leandro Lima]

Hello Jordan.

I think SVDetect can help you.

[Jordan]

Thanks Leandro. I'm looking into it now.