Detect LINE1 element in NGS data

Question

[raipergm34]

Hi,

I have task, but I really do not know how to star and what to do. I need to detect LINE1 element in human genom (NGS). LINE1 is copied trought RNA (non-completed fragment without 5` end is created). Any advices? I am really need any advice, I am totaly beginer.

Answer 1

[h.mon]

Have a look at TEToolkik or SalmonTE. I am sure the gtf annotation provided by the TEToolkit team includes LINEs, I believe - but don't know for sure - SalmonTE should also include them.

Answer 2

[Sinji]

HOMER offers a way to download the most recent UCSC reference genome of LINE1 elements (as well as any other transposable elements).