6.2 years ago by
United States
Hi Peter,
I will try to give you my basic understanding of how MACS works. But
before,
I would recommend you to read the MACS Readme
<http: liulab.dfci.harvard.edu="" macs="" readme.html=""> , where you will
find
detailed explanations of how MACS works and what the different output
files
are.
1. I will say that it depends on what you want to do with the
MACS
analysis. Usually, for all the downstream analyses that you can do,
you will
need the interval file (bed). It's just a tab-separated tabular file
that can
be opened with MS Excel anyway. I personally use Excel for quickly
look at
the different FDR. Regarding the slight shift between the positions in
BED or
XLS, this is normal and due to XLS formatting (I believe so)... Here's
the
Readme's explanation: Coordinates in XLS is 1-based which is different
with
BED format.
2. See the MACS paper for a precise answer, but basically, the
negative
peaks are used by MACS to calculate the FDR.
3. The wig files contains both the position of your interval
(your
reads) and a "score". For this reason I like to use it for
visualization of
my data, although it can be also used as input for downstream tools
like CEAS
(gene annotation). Contrary to the wig file, the bed file does not
include a
"score", but only the precise location of your peaks (not reads). As
these
peaks are detected by comparing the reads in your treatment versus
control,
there is only one file (a peak corresponding to a significant
enrichment of
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
can
give you more details if you need to (and more accurate).
Best,
[mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of peter scot
To: galaxy-user@lists.bx.psu.edu
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
second
is peaks.xls the file peaks.xls is same as peaks .intreval file in
the right
out put flow with one bp position added e..g if peak coordinate under
html
report are 99 to 120 than in the peaks .interval it is 100 to 121.
Which one
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
files
one ctrl.wig and another treatment. Wig; Do these two files belong to
ctrl
and treated samples then where are corresponding bed files.
If someone can direct me to the out put as we get in Galaxy while
using MACS
that will be helpful
Thanks
