Given a set of BAM files for single-end reads just mapped with BWA tool, how can I have an overview if the mapping will result in useful information and the quality of the mapping was good? These data is to be used in a ChIP-seq experiment. Because this is a pilot experiment there are no technical duplicates, only one BAM for the input and for each ChIPed proteins/histone mark. Because of this a "Correlation among samples" plot will not be useful.
I'm new to NGS and ChIP-seq data and I tried to find useful tutorials/ references for galaxy but could not find one dealing with a dataset in a realistic manner.
Which tools and plots should I use? Any general workflow for assessing mapping quality would be appreciated.
EDIT: I would like to have something like the distribution of MAPQ values or the distribution of the reads along the chromosomes.