can someone point to a detailed explanation of how UCSC genome browser interprets coordinates for, and displays, minus strand sequences? It's very confusing. For example this genomic GFF coordinate from mm9 genome:
Pulls out the sequence:
which is correct. However, in the genome browser it appears as the reverse complement going from right to left
- why does it UCSC reverse complement it and display it right to left in this way? What is the logic behind this? Is there a way to reverse it, such that the sequence displayed is the sequence pulled from the genome (i.e.
- I thought UCSC is always BED coordinate based, which is a 0-based coordinate system not 1-based. In that case I would have expected the sequence determined by chr1:3206080-3206102 (meant to be a GFF coordinate) to be one base shorter than the sequence I get from UCSC, i.e. chr1:3206080-3206102:- in BED should have a minus 1 start, yielding chr1:3206079-3206102:-
any intuitive explanation of how to think about UCSC orientation display choices and how that connects to sequences and their reverse complement on minus strand (and where/when BED versus GFF conventions are used) would be very helpful.