Question: Pipeline for detecting (TF) Chip-seq peaks in transposable elements?
1
gravatar for Biojl
2.5 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

Hi,

Anyone knows a good pipeline to call TFBS peaks using chip-seq data in transposable elements? Most of the traditional pipelines rely on uniquely mapped reads, and obviously there are a depletion of peaks in TEs as a consequence.

I've located two potential softwares for the alignment part:

I was wondering if someone has more up-to-date recommendations and other softwares for other parts of the pipeline (i.e. is macs2 a good option?)

Thanks in advance

ADD COMMENTlink modified 4 weeks ago by miller.uthscsa20 • written 2.5 years ago by Biojl1.7k
1

Could give RepEnrich a try.

ADD REPLYlink written 2.5 years ago by Sinji2.9k

I am interested in particular copies, not family enrichment. Therefore I want to call peaks at specific locations.

ADD REPLYlink written 2.5 years ago by Biojl1.7k
2
gravatar for miller.uthscsa
4 weeks ago by
miller.uthscsa20 wrote:

I have been looking for one for a while, but I don't think it really exists yet. I know the Hammell lab is working on one called TEpeaks (https://github.com/yingjin07/TEpeaks). Also there was a recent study which did this using a custom pipeline https://www.nature.com/articles/s41467-018-08006-y

ADD COMMENTlink written 4 weeks ago by miller.uthscsa20
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