Question: what's 5th column of MACS peak calling output?
gravatar for Daofeng Li
4.3 years ago by
Daofeng Li40
Daofeng Li40 wrote:


Is the 5th column of peak calling the -log10 pvalue?

chr1    9845    10903   MACS_peak_1     252.67

chr1    725774  727158  MACS_peak_2     70.11

chr1    818085  818767  MACS_peak_3     91.28



chip-seq • 1.5k views
ADD COMMENTlink modified 4.3 years ago by Jennifer Hillman Jackson25k • written 4.3 years ago by Daofeng Li40
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


In short, yes. But I'll explain how I knew for next time you run across something like this. There are usually clues in the output files from tools, or help in the documentation, and how to look through these is worth sharing.

This is output from tool wrapper version "MACS (version 1.0.1)" on the public Main instance, other wrappers may differ in output and/or the underlying version of MACS.

With a primary BED dataset is like this:

track name="MACS peaks for MACS_in_Galaxy"
chr19 3204536 3204745 MACS_peak_1 171.68
chr19 3208324 3208554 MACS_peak_2 118.93
chr19 3210881 3211039 MACS_peak_3 59.26


And the associated "peaks" BED dataset is like this (disregarding other header lines):

#chr start end length summit tags -10*log10(pvalue) fold_enrichment FDR(%)
chr19 3204536 3204745 209 105 15 171.68 50.40 0.00
chr19 3208324 3208554 230 127 11 118.93 37.09 0.00
chr19 3210881 3211039 158 80 4 59.26 24.81 5.76


The two can be compared and the value determined. Some tools have more 3rd party documentation than others. The MACS doc link (from the tool form) describes the files, but not the exact contents in detail, probably because the output files are already labeled.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Jennifer Hillman Jackson25k
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