I have two questions about BED files that contains strand information as "+" and "-". However, they are not same as transcribed strand (TS) or non-transcribed strand (NTS), right? I am very confused.

For example; a BED6 file contains 6 columns with strand information;

chr1    3214481 3671498 NM_001011874    0   -

I have also a bam file and used bedtools coverage according to this bed file and got this (first line):

chr1    3214481 3671498 NM_001011874    0   -   0.0083454

Q1: One gene always have a transcribed strand and a non-transcribed strand part, however it can be located on either - or + strand. How can one extract information about its strand information except transcribed or non-transcribed from bam file?

Q2: What does bedtools coverage give us? How can we normalize it to, let's say, RPKM?

Q3: When I got TS/NTS information, I need to calculate coverage again according to this information. But how? (Basically, first question.)

Thank you in advance.