Detect LINE1 element in NGS data
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3.6 years ago
raipergm34 • 0

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.

LINE1 RNA NGS fragment • 924 views
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3.6 years ago
h.mon 33k

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.

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3.6 years ago
Sinji ★ 3.1k

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

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