where can i find all TE elements GTF? · Biostar

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where can i find all TE elements GTF?

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?

peakcalling rnaseq clipseq

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updated 4.5 years ago by Michael Dondrup

• written 4.5 years ago by PK •

1 answer

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.

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written 4.5 years ago by Michael Dondrup

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