4.3 years ago by
United States
Hello,
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 http://usegalaxy.org, 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
