Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
I've got some ATACseq peak files that I've generated (both from Homer and MACS2, in case one is preferred). I am wanting to generate a Venn diagram to compare/contrast these peaks. How might I be able to do this? I was hoping to then put this input file into an interactive app like from here:
https://asntech.shinyapps.io/intervene/
The example dataset used on the above website is:
mESC pro-B Myotube Th-cell
NM_001081209 NM_008922 NM_133810 NM_001109661
NM_133833 NM_008922 NM_028133 NM_028331
NM_015818 NM_145996 NM_010866 NM_016754
NM_015818 NM_019790 NM_026830 NM_007598
NM_018872 NM_033563 NM_028040 NM_008856
NM_001005423 NM_027456 NM_001163360 NM_001081345
NM_008342 NM_027966 NM_178665 NM_010735
NM_025386 NM_008972 NM_022318 NM_001162366
NM_010262 NM_010566 NM_015740 NM_024214
NM_023755 NM_177646 NM_175418 NM_021782
For reference, my own peak files look something like this (from Homer):
#PeakID chr start end strand score focus ratio/other Total Tags Background Tags Fold Change vs. Background p-value
Merged-VHII01000031.1-133075-1 VHII01000031.1 133025 133125 + 463 0 1499.5 215.9 6.94 0.00E+00
Merged-CM020919.1-145512-1 CM020919.1 145462 145562 + 285.5 0 53 8.3 6.37 4.01E-25
Merged-CM020928.1-3483966-1 CM020928.1 3483916 3484016 + 188.4 0 422 22.5 18.74 0.00E+00
Merged-CM020931.1-7099184-1 CM020931.1 7099134 7099234 + 163.7 0 380 69 5.5 9.51E-149
Merged-VHII01000031.1-132864-2 VHII01000031.1 132797 132932 + 162.6 0 1711.5 248.2 6.89 0.00E+00
Merged-CM020911.1-23060979-1 CM020911.1 23060929 23061029 + 157.7 0 398.5 45.5 8.75 4.93E-224
Merged-CM020922.1-34104023-1 CM020922.1 34103973 34104073 + 150.7 0 40 2.4 16.34 4.03E-34
Merged-CM020920.1-21165501-1 CM020920.1 21165451 21165551 + 131.7 0 186 25 7.45 1.80E-94
Merged-CM020925.1-35916431-1 CM020925.1 35916381 35916481 + 129.3 0 267 64.6 4.13 7.97E-79
Merged-CM020921.1-28176661-2 CM020921.1 28176578 28176745 + 124.4 0 689.5 72 9.58 0.00E+00
This is just a merged file of one type of tissue (I have three total).
Thanks in advance for any insights you might be able to provide.
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Something more global and useful based on positions: https://bedtools.readthedocs.io/en/latest/content/tools/jaccard.html
That might be useful.