Question: CCDS coordinates confusion with UCSC & NCBI
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:

ADD REPLYlink written 3.0 years ago by Kevin Blighe66k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1979 users visited in the last hour