where can i find all TE elements GTF?

Question

[PK]

Hi all,

I want to quantify the expression repeat elements expression for my Clip-seq experiment. So I took multi-mappers and wants to quantify. For that where can i find RE elements GTF (human) file?. or else can i map against genome and call the peaks?. if so what are the parameters do i have to use while mapping (bwa-mapping)? ..There are so many articles out there but most of them build their own gtf file. can you please suggest some article?

Answer 1

[Michael]

See Quantifying repetitive elements from RNA-seq (hisat2 or Salmon)

On the web-page of TEtranscript, you will find links to download annotation files containing repeats.