I need help or advice in the following questions which may not be related to each other but are all important for the analyses that I'm currently working on. I'm analyzing my ATAC-seq and ChIP-seq data as well as correlating them to my RNA-seq data.
1) When I use HOMER annotatePeaks.pl or findMotifGenome.pl) to search for the occurrence of my motif of interest in 3 peak files generated from 3 biological replicates, I found that in the positive control sites (that showed peak enrichment in all 3 libraries) showed up only in 1 library and not the other two despite similar enrichments in all 3 libraries at the same site. A check with other expected sites showed the same as well (some in 2 libraries and not the other). It seems like HOMER 'randomly' selected sites that showed enrichment in that motif in the 3 libraries and did not report all enriched sites like it's supposed to.
2) I would like to correlate enriched peaks (ATAC-seq or ChIP-seq) to my RNA-seq data i.e. correlate enriched peaks to expressed genes/TSS.
3) How do I add in conservation as a filter to enriched sites containing my motif of interest (in HOMER or other recommended programs)?
Would appreciate any help or advice given for the above questions. Thanks a million!