Question: Pipeline transposable elements
1
gravatar for SeaStar
8 days ago by
SeaStar10
Ocean
SeaStar10 wrote:

Hello! I'm searching for suggestion about the new best pipeline/s to find TRANSPOSABLE ELEMENTS in a new assembled genome of a no reference species (octopus). I don't want to use repeatmasker. Can anyone help me?

transposon • 117 views
ADD COMMENTlink modified 3 days ago by Beuss110 • written 8 days ago by SeaStar10

There is nothing wrong with RepeatMasker but it is indeed not a tool to find "new" repeats. You should use if for what's intended for namely masking of a genome using a library of TEs

ADD REPLYlink written 8 days ago by lieven.sterck4.8k
2
gravatar for flogin
8 days ago by
flogin80
FioCruz/Brazil
flogin80 wrote:

If you had the NGS datasets of its genome you can use the DNApipeTE (https://github.com/clemgoub/dnaPipeTE) or for your assembled genome you can use the TEdenovo and TEannot pipelines from REPET package (https://urgi.versailles.inra.fr/Tools/REPET).

ADD COMMENTlink written 8 days ago by flogin80
1
gravatar for Beuss
3 days ago by
Beuss110
France
Beuss110 wrote:

RepeatMasker is a viable solution if you already have a database of TEs from a very close specie. With RepeatMasker and Repbase, you won't be able to detect all mobile elements specific to your newly assembled genome. Moreover, your annotation will be polluted by false positive.

REPET perform de novo detection by only using the genome sequence. It's quite heavy computation, but if your genome is too big or too repeated, you could apply an iterative strategy to reduce complexity. This way you will find the specific population of TE for your genome and do an exhaustive annotation of all the copies even for the very oldest ones.

https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0150-y

https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7562280

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0016526&type=printable

ADD COMMENTlink written 3 days ago by Beuss110
1

A pain to install, still waiting for a proper container.

ADD REPLYlink written 3 days ago by Juke-342.2k
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