I need help with Galaxy-Macs' Peak Calling tool.
Using my ChIP-Seq data (Experimental and input), I mapped the reads with bowtie and did the peak calling with Macs. But something doesn't look right. First of all, according the 'Peaks:interval' file, there is only 3000~ peaks that were picked up with all of their FDR equals 100%. And the largest fold enrichment was only 17X. Also, one of the target with the highest fold enrichment from the previous ChIP-Seq (this is my second ChIP-seq repeat) wasn't there in my peaks:interval file. Second, I knew these won't right, so I took a look at it in UCSC genome browser after converting it to BigWig file. There, I looked at that target gene with the highest fold enrichment from the previous ChIP-Seq and there was a robust peak with fold enrichment greater than 70. Why doesn't my peaks:interval file contain target genes with significant fold enrichment like this and just contain 3000~ genes with 100% FDR and lower fold enrichment?
To me, it looks like something went wrong with the Peaks:interval file during my Peak calling analysis, while files such as peaks;bed file to visualize it under genome browser is perfectly fine. I repeated several times but all I get is the same weird results.
Could anyone please help/guide/instruct/tip me with what could possibly going on with my peak calling analysis?