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, From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of peter scot Sent: Tuesday, September 11, 2012 12:45 PM 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