I am relatively new to NGS analysis and I feel as though I am getting in over my head. I have watched several tutorials, but I can't seem to find information/examples of the kind of analysis that I am interested in doing. I am hoping that someone here might be able to help me out. Our bioinformatics core is very good, but I would like to learn this analysis myself because it will definitely be a good skill to have in the future.

Our lab has recently used MNase-seq with the hopes of looking at changes that occur in chromatin organization under a variety of conditions. What we would like to do is compare changes that occur in our control vs. treated samples. We are interested in global changes such as gain/loss of peaks as well as changes in peak intensity and peak width. I would also like to cross reference these changes with a published ChIP-seq track of our favorite transcription factor to see if these changes occur more preferentially in the vicinity of these transcription factor binding sites.

So far I have been using Galaxy for my analysis. I have the data files from the bioinformatics core in .bed, .bam, .bai, and .fastq formats. I have also looked at the bam files in IGV and have done some manipulations (intersect/window/subtraction) using the bedtools options, but I haven't been able to produce an actual file of these manipulations to do any sort of statistical analysis/comparison. In Galaxy I haven't been able to do much with any these files since Galaxy doesn't seem to recognize the formats despite trying several conversions. I appreciate any input or suggestions that you can offer. In the meantime I will continue plugging away with my data and see if I can figure this out.