5.4 years ago by
I will try to give you my basic understanding of how MACS works. But
I would recommend you to read the MACS Readme
<http: liulab.dfci.harvard.edu="" macs="" readme.html=""> , where you will
detailed explanations of how MACS works and what the different output
1. I will say that it depends on what you want to do with the
analysis. Usually, for all the downstream analyses that you can do,
need the interval file (bed). It's just a tab-separated tabular file
be opened with MS Excel anyway. I personally use Excel for quickly
the different FDR. Regarding the slight shift between the positions in
XLS, this is normal and due to XLS formatting (I believe so)... Here's
Readme's explanation: Coordinates in XLS is 1-based which is different
2. See the MACS paper for a precise answer, but basically, the
peaks are used by MACS to calculate the FDR.
3. The wig files contains both the position of your interval
reads) and a "score". For this reason I like to use it for
my data, although it can be also used as input for downstream tools
(gene annotation). Contrary to the wig file, the bed file does not
"score", but only the precise location of your peaks (not reads). As
peaks are detected by comparing the reads in your treatment versus
there is only one file (a peak corresponding to a significant
reads that is not present in the control sample in one locus).
I hope I was able to help you... I'm sure a lot of people on this list
give you more details if you need to (and more accurate).
[mailto:email@example.com] On Behalf Of peter scot
Subject: [galaxy-user] MACS out put files from Galaxy
I ran MACS on my chipseq dataset and found various files:
1. under html report there ar etwo files one of negative peaks.xls and
is peaks.xls the file peaks.xls is same as peaks .intreval file in
out put flow with one bp position added e..g if peak coordinate under
report are 99 to 120 than in the peaks .interval it is 100 to 121.
should be followed?
2. What is the meaning of negative peak. interval file?
3. I have used ctrl and treated sample to run MACS - there are two wig
one ctrl.wig and another treatment. Wig; Do these two files belong to
and treated samples then where are corresponding bed files.
If someone can direct me to the out put as we get in Galaxy while
that will be helpful