I was trying to obtain nucleosome positioning bigwigs files using a bam file from MNase-seq data obtained by paired end sequencing and I keep getting a regular bigwig file for nucleosome occupancy. What parameters are important to set to get counted only the 3 nucleotides at the center of each fragment?
Please see the tools under the section deepTools in the tool panel for many options for filtering or summarizing bigWig files.
Thanks for the suggestion. Can you be more specific?
Pick a deepTools tool, scroll down to the Help section, and you’ll find links to the Galaxy tutorials plus the original author resources. Those will describe the possible manipulations. This is unlikely to involve just one tool.
I can’t provide specific help for whatever tool you were using originally since it wasn’t specified. But in general, if you want your data filtered for a specific set of genomic coordinates, then you’ll need to provide those coordinates to the tool. Usually, that is in a BED input file but not always.