This is somewhat of a naive question.
I've been using MACS2 on galaxy to call peaks on my ChIP-seq BAM. files as is the usual.
Recently though I performed the MACS2 filterdup function, to filter out any duplicates I have; this outputs BED. files of my reads.
Is it okay to use the BED. Files to call peaks or should I convert the BED. files to BAM. and then run MACS2?
Thanks in advance for your help.