After peak calling using MACS2, I ran two footprinting packages, RGT-HINT and CENTIPEDE. What is the best way to compare the results across these two and find concordance (common motifs)? CENTIPEDE seems to give a much larger range between start and stop coordinates (50 - 200 bp) but HINT gives the range which matches the length of the motif ( 8-12 bp).
CENTIPEDE final output (notice start and stop):
chr1 3210609 3210827 ZBT17_MOUSE.H11MO.0.A
chr1 3210610 3210824 ZN148_MOUSE.H11MO.0.D
chr1 3210611 3210825 KLF5_MOUSE.H11MO.0.A
chr1 3210611 3210830 WT1_MOUSE.H11MO.0.B
chr1 3210613 3210829 SALL1_MOUSE.H11MO.0.D
chr1 3210615 3210836 MAZ_MOUSE.H11MO.0.A
chr1 3210616 3210834 KLF15_MOUSE.H11MO.0.A
chr1 5056171 5056379 LHX6_MOUSE.H11MO.0.C
chr1 5056179 5056403 BRAC_MOUSE.H11MO.0.B
chr1 5056182 5056402 STAT1_MOUSE.H11MO.1.A
HINT final output (notice start and stop):
chr1 3210395 3210402 UBIP1_MOUSE.H11MO.0.D
chr1 3210444 3210452 HXD4_MOUSE.H11MO.0.D
chr1 3210639 3210646 ZN335_MOUSE.H11MO.1.A
chr1 3210640 3210651 SUH_MOUSE.H11MO.0.A
chr1 3210677 3210689 MEIS1_MOUSE.H11MO.0.A
chr1 3210677 3210690 HXB6_MOUSE.H11MO.0.D
chr1 3210715 3210737 MAZ_MOUSE.H11MO.0.A
chr1 3210715 3210726 MAZ_MOUSE.H11MO.1.A
chr1 3210715 3210726 WT1_MOUSE.H11MO.1.A
chr1 3210714 3210724 SALL4_MOUSE.H11MO.0.A
Due to this, we end up having multiple motifs from HINT for a single region in CENTIPEDE. Has anyone compared these two packages before? What would be the best way to go about comparing these two outputs in order to look for consensus among these two packages? Generally speaking, what is the ideal way to compare output from packages that do footprinting/motif calling analysis?
