Snps At Tf Motifs

Question

[Ming Tommy Tang]

Hi,

I have a bed peak file from the ChIP-seq experiment (around 200bp each interval) . how can I find the motifs in each interval and output to a bed file?

I then can intersect it with the SNP bed file using bedtools.

Thanks!

Answer 1

[PoGibas]

If I understood correctly:

• You have genomic intervals and want to identify common motifs between them. If so, then:

  1. Use bedtools getfasta to extract sequences for each of the intervals in a BED file.

     bedtools getfasta -fi GENOME.fa -bed ChIP-seq.bed -fo ChIP-seq.fa
     

  2. Use MEME to analyze your sequences (ChIP-seq.fa) for shared pattern (motif).

• You have SNP bed and want to see in those SNPs overlap binding sites. If so, then:
  all you need is bedtools intersect to screen for overlaps between SNPs and ChiP-Seq peaks.

  bedtools intersect -a ChIP-seq.bed -b SNP.bed
  

[Ming Tommy Tang]

I want to have the intervals of the all the TF motifs that occur at the ChIP-seq bed file, and then intersect the motif coordinates with the SNP coordinates. Can MEME do it? Thank you for your response.

[PoGibas]

Ok, now I get it. You can still use MEME. Output will look like this example MEME output. Extract motif start position and add motif length to it.

[Ming Tommy Tang]

I was wondering if there any software can do it automatically, thanks!