Hi, we use MACS to call peaks for all of our ChIP-seq data and it has never given us any problems. With our most recent dataset, MACS outputs the same number and coordinates of peaks regardless of different input files or even if no input is used. This occurs even when using past ChIP-seq experiments files. Obviously MACS is not using/recognizing the Input files during the peak calling, even though past data was successfully processed before. Can anyone suggest what may be occurring?
Work Flow: Experiment Name MACS in Galaxy Paired End Sequencing Single End ChIP-Seq Tag File select at runtime ChIP-Seq Control File select at runtime Effective genome size 2700000000.0 Tag size 50 Band width 300 Pvalue cutoff for peak detection 1e-05 Select the regions with MFOLD high-confidence enrichment ratio against background to build model 10 Parse xls files into into distinct interval files True Save shifted raw tag count at every bp into a wiggle file Do not create wig file (faster) Use fixed background lambda as local lambda for every peak region True 3 levels of regions around the peak region to calculate the maximum lambda as local lambda 1000,5000,10000 Build Model Do not build the shifting model Arbitrary shift size in bp 75 Diagnosis report Do not produce report (faster) Perform the new peak detection method (futurefdr) False