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Help With Understanding Macs Output. What Does Tags And Summit Exactly Mean?

Hi,

I'm using MACS for my chip-seq analysis. I'm a bit confused on what tags and summit mean in the output file (peaks.xls). Here is a typical output:

chr    start    end    length    summit    tags    #NAME?    fold_enrichment    FDR(%)
chrI    2179888    2179989    102    57    41    741.77    338.24    0
chrIV    6576127    6576187    61    30    25    561.15    306.48    0
chrII    7123680    7123731    52    26    24    638.77    266.85    0

My understanding is that, tags means reads. What does the number of tags here represent? The control or treatment? And also does summit just mean, the point at which the peak is the highest? In chr I, does summit exist at 2179944 (2179888+57 - 1)?

Thanks!

macs peak-calling chip-seq
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updated by Ram Ram • written by Jordan Jordan

1 answer

  • Tags: Number of reads within the peak.
  • NAME_peaks.xls, are the peaks found in 'Treatment' but not in 'control' (enriched regions), while NAME_negative_peaks.xls, are the peaks found in 'control' but not in 'treatment' (reduced regions).
  • Summit: base position (from peak start) at which peak is highest.
  • Not sure on the last one, maybe you're correct.

edit: corrected summit!

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written by arnstrm arnstrm

For tags, when you say number of reads within the peak, do u mean the reads that belong to treatment or control, or both?

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written by Jordan Jordan

I'm not sure but since it's the difference (normalized reads in treatment - normalized reads in control), it could be just a number(?)

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written by arnstrm arnstrm

MACS has another output file named NAME_summits.bed

As its annotation: NAME_summits.bed contains the peak summits locations for every peaks. The 5th column in this file is the summit height of fragment pileup. If you want to find the motifs at the binding sites, this file is recommended.

I want to ask what does this summit height mean? Does it mean the number of reads in the summit position?

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updated by Ram Ram • written by camelbbs camelbbs

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