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Coordinate system 0-based or 1-based?

asked 2014-04-01 18:36:02 -0700

Aliz Rao gravatar image

Should I use a 0-based or 1-based coordinate system when creating a custom annotation track? E.g. to indicate a single nucleotide, should the posstart and posend column be identical (1-based system) or should they differ by one (0-based system)?

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answered 2014-04-04 15:13:03 -0700

Hi Aliz,

Currently in our analysis software SVS 8 (soon to be in GenomeBrowse 2.0!), there are three options for how the coordinates can be classified. The differences between these options result in different widths of the created features.

0-Based Interval (Half-open Interval): Here you have both a Start and a Stop position field and the width of the created feature would be Stop - Start, and the smallest start can be zero.

1-Based Interval (Indexed Interval): Here you have both a Start and a Stop position field and the width of the created feature would be Stop - Start + 1, and the smallest start can be one.

Position (1bp width): Here you have a single position field and it assumed that the width of every feature would be 1bp.

You can use any of these options to create a single nucleotide track, the simplest is the Position option where the position column selected should represent the location of the nucleotide on the chromosome.

Please let me know if you have any further questions.

Thanks, Jami...

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Asked: 2014-04-01 18:36:02 -0700

Seen: 3,548 times

Last updated: Apr 04 '14