This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Detect LINE1 element in NGS data

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
• 2,142 views • link
updated by Sinji Sinji • written by raipergm34 • raipergm34

2 answers

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.

• 0 views • link
written by h.mon h.mon

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

• 0 views • link
written by Sinji Sinji

Log in to answer this question.

More posts like this