Question: Snps At Tf Motifs
0
gravatar for Ming Tang
5.0 years ago by
Ming Tang2.4k
Houston/MD Anderson Cancer Center
Ming Tang2.4k wrote:

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!

chip-seq snp • 1.7k views
ADD COMMENTlink modified 5.0 years ago by PoGibas4.7k • written 5.0 years ago by Ming Tang2.4k
0
gravatar for PoGibas
5.0 years ago by
PoGibas4.7k
Vilnius
PoGibas4.7k wrote:

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
    
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by PoGibas4.7k

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.

ADD REPLYlink written 5.0 years ago by Ming Tang2.4k

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.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by PoGibas4.7k

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

ADD REPLYlink written 5.0 years ago by Ming Tang2.4k
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