From bed file to enrichment score
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6.8 years ago
GK1610 ▴ 110

I have a consensus peak bed file for which I have to quantify the enrichment score of a bam file against their respective control file. What is the best way in macs2 software or any other software to get enrichment scores of given bed file?

Also, is the col. 7 in macs2 narrowpeak file is the enrichment score for a given peak regions averaged over the width of the peak?

ChIP-Seq • 1.7k views
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The enrichment comes from the position with the highest fragment pileup in the ChIP against the local control lambda, so no, the width is not directly of relevance for the enrichment. Check in the original paper, it is quiet intuitive to read.

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