I'm trying out differential binding analysis with macs2 bdgdiff. I've called peaks and gotten very reasonable values for fold-changes, p-values, q-values, etc. For example:
treat1_chip_repB.bed
1 10006 10499 treat1_chip_repB_peak_1 109 . 2.80877 14.06537 10.98392
1 46683 47046 treat1_chip_repB_peak_2 46 . 3.94851 7.41653 4.69998
1 180768 181015 treat1_chip_repB_peak_3 32 . 2.89084 5.85297 3.29158
1 199870 200048 treat1_chip_repB_peak_4 26 . 3.09339 5.16864 2.68865
1 358746 359816 treat1_chip_repB_peak_5 44 . 4.02818 7.07086 4.41624
1 394998 395443 treat1_chip_repB_peak_6 19 . 3.15028 4.30817 1.91544
1 450607 451066 treat1_chip_repB_peak_7 18 . 3.09737 4.20707 1.85041
1 588143 588508 treat1_chip_repB_peak_8 28 . 3.55979 5.34418 2.82556
1 590955 591428 treat1_chip_repB_peak_9 32 . 3.20037 5.81651 3.26295
1 623994 624155 treat1_chip_repB_peak_10 23 . 3.24114 4.74840 2.32049
. . .
. . .
treat2_chip_repB.bed
1 9982 10520 treat2_chip_repB_peak_1 325 . 4.51491 35.86348 32.59083
1 11213 11689 treat2_chip_repB_peak_2 31 . 3.22501 5.38701 3.18507
1 13482 14198 treat2_chip_repB_peak_3 32 . 2.81719 5.44192 3.23710
1 29155 29325 treat2_chip_repB_peak_4 12 . 2.53058 3.23237 1.29448
1 46687 47138 treat2_chip_repB_peak_5 123 . 5.60019 15.02273 12.31674
1 89078 89436 treat2_chip_repB_peak_6 15 . 2.65434 3.51344 1.52353
1 91051 91364 treat2_chip_repB_peak_7 13 . 2.66162 3.34514 1.36895
1 180765 181094 treat2_chip_repB_peak_8 112 . 4.36022 13.94062 11.26981
1 184508 184657 treat2_chip_repB_peak_9 38 . 2.76260 6.11458 3.85310
1 199058 200002 treat2_chip_repB_peak_10 26 . 3.03284 4.81645 2.68143
. . .
. . .
However, I'm getting crazy values for the log-likelihoods produced by macs2 bdgdiff.
diff_treat1_repB-vs-treat2_repB_c3.0_common.bed
1 9999 10495 diff_treat1_chip_repB-vs-treat2_chip_repB_common_1 -5626780945305257054830592.00000
1 46752 47031 diff_treat1_chip_repB-vs-treat2_chip_repB_common_2 -8612834383639687743930368.00000
1 180771 180951 diff_treat1_chip_repB-vs-treat2_chip_repB_common_3 -14910970167988796344238080.00000
1 359329 359497 diff_treat1_chip_repB-vs-treat2_chip_repB_common_4 -14372019716837756622602240.00000
1 590976 591413 diff_treat1_chip_repB-vs-treat2_chip_repB_common_5 -7164430050156399653027840.00000
1 779550 779705 diff_treat1_chip_repB-vs-treat2_chip_repB_common_6 -16340788830357069758464000.00000
1 804823 804947 diff_treat1_chip_repB-vs-treat2_chip_repB_common_7 -20745697224011715050471424.00000
1 812089 812380 diff_treat1_chip_repB-vs-treat2_chip_repB_common_8 -16801092741071353413632000.00000
1 815171 815897 diff_treat1_chip_repB-vs-treat2_chip_repB_common_9 -3286164094130363687763968.00000
. . .
. . .
•
written
by
ariel.balter
1 answer
It is indeed an overflow issue most probably by the incorrect-compiled-dependenies. I used macs2.1.0 and it works perfectly one year before. But recently I met the same issue. I was troubleshooting several days until I noticed that I have unmatched numpy and python from miniconda env installed several months before (macs2 was installed before by root without miniconda env). Now I fixed this issue by creating a new conda env and installing macs2 there. See the link: https://github.com/taoliu/MACS/issues/156
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Hi
I am getting the same weird results. It's a very strange thing, since the bdgdiff function should have a default threshold for this ratio (logLR > 3). So negative values should be removed by default.
Have you managed to solve the issue? I'm interested too!
Best, Moreno