Snps At Tf Motifs
1
0
Entering edit mode
7.6 years ago
Ming Tang ★ 2.6k

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!

snp chip-seq • 2.3k views
ADD COMMENT
0
Entering edit mode
7.6 years ago
PoGibas 4.9k

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2222 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6