BAM file containing ALL reads, next step?

[chipnewb]

Hi guys, I'm new to this forum and new to ChIP-seq so forgive my ignorance and the broadness of my question.

I recently obtained two bam files from a company which states that the files they provide are, "a binary alignment/map file which includes all reads. Predefined columns within the file will flag sequence reads which passed or failed chastity filtering, and mark those reads which are unique and have either multiple, or no matches".

My goal is to look at differences in peaks between the two files (treatment vs control) and for this I have Partek Genomics Suite. Currently, I am able to simply load the bam files into Partek, generate peaks, have them annotated and look at fold difference between treatment and control.

My question is would it be wiser to first "clean up" the bam files since they apparently contain ALL reads, not just those that were high quality and aligned, and then import them into Partek? For example, should I remove all those reads which failed chastity filtering as well as those that have no matches, etc?

Thanks for your time