Q:
I tried to use your ACT software for aggregation plot and slightly confused.
If it’s possible can you please look at my input (at the end of this email) and
tell me where I have misunderstanding?

1) Why position -2 (-15bp) has signal 6.7 instead of (10+5+7)/3=7.3?
2) Why positions <-2 (25bp away) have any values and how these values were obtained (as my signal is only up to 17bp)?
3) How values for -1 and 0 were obtained?

Thank you in advance,
Hennady.

bed.txt

chr1 20 25 +
chr1 280 288 +

signal.txt

chr1 1 10
chr1 2 5
chr1 3 7
chr1 300 6
chr1 301 8
chr1 302 9

execution
-bash-3.2$ python ACT.py –nbins=10 –mbins=0 –radius=100 bed.txt signal.txt
# ACT.py –nbins=10 –mbins=0 –radius=100 bed.txt signal.txt
# annotationCount: 2
Bin Center mean stdev
-10 -95 3.5 0.0
-9 -85 3.5 0.0
-8 -75 3.5 0.0
-7 -65 3.5 0.0
-6 -55 3.5 0.0
-5 -45 3.5 0.0
-4 -35 3.5 0.0
-3 -25 3.5 0.0
-2 -15 6.7 3.12889756943
-1 -5 7.0 0.0
0 4 7.0 0.0
1 14 7.0 0.0
2 24 7.8 3.69684550214
3 34 8.0 1.41421356237
4 44 8.0 1.41421356237
5 54 8.0 1.41421356237
6 64 8.0 1.41421356237
7 74 8.0 1.41421356237
8 84 8.0 1.41421356237
9 94 8.0 1.41421356237

A:
The default for ACT is to assume that the signal file is a step-wise signal input, so for example in your signal.txt file, all positions on chr1 between nucleotides 3 and 300 are assigned the value 7 (hence it is not acting as your calculation below might suggest).

In addition, your bed file has two annotations (20 to 25 and 280 to 288, both +). For the positions <-2 bins away, only the values upstream of the 280 to 288 annotation are used.