Normalize reported bedtools coverage (10th column)

Question

[biotech]

I would like to normalize 'blockCount' field in 'coverage_1_2.txt' bed file, coming from:

bedtools coverage -b MZ123.aligned.q30.bam -a 7a1.bed -counts > coverage_1_2.txt

I provisionally normalized by dividing mapping reads (blockCount) between the size of the interval (protein size).

Note that this is not RNA-seq data. I'm not trying to compare samples gene expression. I mapped DNA vs DNA. Want to know if I have overrepresented sequences in my library.

Here are the headers of the files:

7a1.bed

track name=A. citrulli 7a1 genome description="A. citrulli 7a1 genes" itemRgb=On
Ga0114182_11    1   865 Ga0114182_111   1000    +   1   865 65,105,225
Ga0114182_11    841 2053    Ga0114182_112   1000    -   841 2053    65,105,225
Ga0114182_11    2174    2759    Ga0114182_113   1000    -   2174    2759    65,105,225
Ga0114182_11    2755    3886    Ga0114182_114   1000    -   2755    3886    65,105,225
Ga0114182_11    4008    4587    Ga0114182_115   1000    -   4008    4587    65,105,225
Ga0114182_11    5047    5419    Ga0114182_116   1000    +   5047    5419    65,105,225
Ga0114182_11    5681    6212    Ga0114182_117   1000    +   5681    6212    65,105,225
...

coverage_1_2.txt

Ga0114182_11    1   865 Ga0114182_111   1000    +   1   865 65,105,225  150
Ga0114182_11    841 2053    Ga0114182_112   1000    -   841 2053    65,105,225  290
Ga0114182_11    2174    2759    Ga0114182_113   1000    -   2174    2759    65,105,225  127
Ga0114182_11    2755    3886    Ga0114182_114   1000    -   2755    3886    65,105,225  244
Ga0114182_11    4008    4587    Ga0114182_115   1000    -   4008    4587    65,105,225  173
Ga0114182_11    5047    5419    Ga0114182_116   1000    +   5047    5419    65,105,225  136
Ga0114182_11    5681    6212    Ga0114182_117   1000    +   5681    6212    65,105,225  132
Ga0114182_11    6324    7119    Ga0114182_118   1000    -   6324    7119    65,105,225  216
Ga0114182_11    7153    7771    Ga0114182_119   1000    -   7153    7771    65,105,225  152
...