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.
