CCDS coordinates confusion with UCSC & NCBI
Hi, guys. I've been dealing with CCDS data to find CDS regions. I found that in CCDS data, cds region coordinates were not like what I thought to be 0-based or 1-based coordinates. For example:
4 NC_000004.12 ADD1 118 CCDS3364.1 Public + 2875915 2928170 [2875915-2876109, 2881897-2882059, 2884514-2884665, 2894012-2894092, 2894581-2894730, 2898183-2898326, 2898432-2898530, 2899258-2899434, 2904763-2905107, 2907742-2907843, 2908514-2908603, 2914883-2915039, 2926013-2926111, 2926641-2926674, 2928170-2928170] Identical
In the line CCDS3364.1, the last cds region was 2928170-2928170, if 0-based the length of this region was "2928170 minus 2928170 equals 0", but the fact was that one "A" base was there. if 1-based the UCSC data gave the coordinats 2928171-2928171. That made me confused.
Did I need to plus 1 to the CCDS data cds region end when used as a bed file?
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yanqiangchang •
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Did you obtain this information from the UCSC Table Browser?
The data in the UCSC back-end is 0-based, but it adds 1 to these before displaying in the genome browser.
See here: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1