Snps At Tf Motifs
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.
If I understood correctly:
You have genomic intervals and want to identify common motifs between them. If so, then:
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
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
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