Question 1: I'm confused about definition of types of strand and cannot find any official document about that. So I'm here to verify my understanding about them:
- Forward strand has its left-to-right respective to 5'-to-3'. And reverse strand has its left-to-right respective to 3'-to-5'
- Plus (or positive) strand is equivalent to forward strand. Minus (or negative) strand is equivalent to reverse strand
- Sense strand means it has mRNA part. Antisense strand is complementary information to sense strand which has no mRNA part. Sense strand can be on either forward (positive,plus) strand or reverse (negative, minus) strand.
- Coding strand is equiavalent to sense strand. Template strand is equivalent to antisense strand.
Question 2: Is information about reverse/forward strand in flag of SAM file equivalent to above definition of strand? Especially in result by STAR alignment.
Question 3: Does all genome database store position in term of forward strand only? For example, ensembl.
And if possible, can anyone of you share with me any official document about these things?
Thanks in advance for any help.