TAIR10.org's GBrowser is 1-based or 0-based coordinate system? ! I am totally confused.
For example, I want to have 3rd to 7th base: 3,4,5,6,7. All 5 bp.
SAM, GFF are 1-based, thus [3, 7]. Clear.
BAM, BED are 0-based, thus [2, 7). Make sense.
The UCSC Genome Browser is uniformly displayed in 1-based way (mentioned in their FAQ http://genome.ucsc.edu/FAQ/FAQtracks#tracks1), also self-explaining. Now I have GBrowser in TAIR10 http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/. Just confused. It's just like [2,8) way.
Here is an example, you could download the gff3 from ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff. And here is an exon:
Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1
Since it is gff file, it means the exon should be [3631, 3913] of one-based, or [3630, 3913) of zero-based. Now turn to get the visualization in GBrowser:
##1. Starts in 3631, good
##2. Ends in 3914, confused...
you could use the ruler to indicate where you are pointing to.
The problem is a matter of display conventions. What you are seeing is the feature going up to and through 3913 but not to 3914. The problem is that the space between where base 3913 starts and ends is usually a pixel or less wide and you don't notice this, but when you are zoomed in base 3913 is a rectangle instead if a pixel and it looks like it "touches" 3914. Does that make sense?
The software is called GBrowse not Gbrowser.
Sorry. I am not at all familiar with Gbrowser. Is it possible to zoom in further to the base level at each end. I can't tell from these images (this resolution) if possibly you just have the ruler lined up with the incorrect position.
Oh, yeah. It makes sense. I need notice the resolution. Thanks for your quick reply~~~