Question: Transcription factor binding sites using ATAC-seq peaks
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gravatar for courtnes
21 months ago by
courtnes0
courtnes0 wrote:

I am working with ATACseq data and pursuant to calling peaks I am interested in identifying transcription factor binding sites using the called peaks. Has anyone had success using TFBS tools, MotifBreakR, or Diffbind to identify transcription factor binding sites and any SNP located in these areas? Are you using any different tools to investigate peaks? I am new here so I appreciate your thoughts

next-gen • 1.2k views
ADD COMMENTlink modified 21 months ago by Batu180 • written 21 months ago by courtnes0
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gravatar for shawn.w.foley
21 months ago by
shawn.w.foley1.2k
USA
shawn.w.foley1.2k wrote:

Personally I use MEME and TOMTOM for calling enriched sequence motifs and intersecting them with known transcription factor binding sites.

Taking your peaks of interest you can convert them into BED format, then use bedtools getfasta to convert them into FASTA format. Running MEME will identify any enriched sequence motifs (it's a nice unbiased method that identifies ANY enriched sequence). Then taking the MEME output you can run TOMTOM to see if any of the sequences that are enriched in your peaks overlap with known transcription factor binding sites.

ADD COMMENTlink written 21 months ago by shawn.w.foley1.2k
1
gravatar for Batu
21 months ago by
Batu180
Batu180 wrote:

I've seen this paper and tool yesterday. Hope they can help.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1642-2

https://github.com/CostaLab/reg-gen#readme

ADD COMMENTlink modified 21 months ago • written 21 months ago by Batu180
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