Question: Detect LINE1 element in NGS data
0
gravatar for raipergm34
9 months ago by
raipergm340
raipergm340 wrote:

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 fragment ngs rna • 381 views
ADD COMMENTlink modified 9 months ago by Sinji2.7k • written 9 months ago by raipergm340
1
gravatar for h.mon
9 months ago by
h.mon19k
Brazil
h.mon19k wrote:

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.

ADD COMMENTlink written 9 months ago by h.mon19k
0
gravatar for Sinji
9 months ago by
Sinji2.7k
UT Southwestern Medical Center
Sinji2.7k wrote:

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

ADD COMMENTlink written 9 months ago by Sinji2.7k
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