BED file should be 0-based, but examples here are 1-based

[hansiu]

Hey,

As detailed here: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED format, including BED3 is 0-based:

• chromStart: The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.

• chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

And in TADtool examples folder both BED files are 1-based (starting with one and the end is included).

So i.e the line: chr12 19975001 20000000 should be: chr12 19975000 20000000

I didn't check the rest of the code but probably this change could affect the algorithms too.

Letting you know to help avoid further users confusion :)

Thank you for developing TADtool! Hania

[vaquerizaslab-old]

Dear Hania,

thank you for your detailed description of the issue. I have just uploaded the latest set of changes, which should also fix this issue. Example files are now BED3 compliant, as is the expected in- and output.

Let us know if you encounter any problems!