Question: Help With Understanding Macs Output. What Does Tags And Summit Exactly Mean?
4
gravatar for Jordan
5.9 years ago by
Jordan1.1k
Pittsburgh
Jordan1.1k wrote:

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 • 5.9k views
ADD COMMENTlink modified 5.9 years ago by arnstrm1.7k • written 5.9 years ago by Jordan1.1k
2
gravatar for arnstrm
5.9 years ago by
arnstrm1.7k
Ames, IA
arnstrm1.7k wrote:
  • 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!

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by arnstrm1.7k

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

ADD REPLYlink written 5.9 years ago by Jordan1.1k

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

ADD REPLYlink written 5.9 years ago by arnstrm1.7k

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?

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by camelbbs650
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