Question: CCDS coordinates confusion with UCSC & NCBI
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gravatar for yanqiangchang
3.0 years ago by
yanqiangchang0 wrote:

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?

assembly • 820 views
ADD COMMENTlink written 3.0 years ago by yanqiangchang0

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

ADD REPLYlink written 3.0 years ago by Kevin Blighe66k
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