IGV load BED track

[Guillermo Marco Puche]

Hello,

My IGV version is 2.3.36.

I'm trying to load a BED on 0 base coordinate system, however it seems that my track line is incorrect.

track name="test" coords=0
chr1 100000 150000

I've tried adding #track and track and using spaces or tabs but none seem to work when I load BED file on IGV.

What I'm doing wrong?

Thanks.

[Jim Robinson]

Hi,

Could you describe the problem in more detail?  Bedfiles are zero base by default, the coords parameter is not neccessary.  So in "normal" human readable coordinates your feature would extend from base 100001 up to but not including base 150000. 

I assume the extension of your file is ".bed",  this is required.

Jim

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[Guillermo Marco Puche]

I'm this is where all the problem comes. 0 based coordinate are not supposed to include from 100000 to 149999?

Following UCSC for BED format:

1. 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.

Maybe it's more "human" to print from 100001 to 149999. However I would like to view BED track from exact coordinates so loading from 100000 to 149999.

[Jim Robinson]

The best way I've found to describe UCSC style bed coordinates is to consider a feature spanning the first base of the genome.  In bed coordinates this feature would have a start of 0 and end of 1.   In gff (and other format) coordinates the feature would have a start of 1 and end of 1.    So

bed:   0-1
gff:    1-1

Is that clear?

Jim

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[xiaol...@gmail.com]

Hi Jim,

I am still confused. For example, if we type chr1:100000-150000 into the search box in the IGV toolbar and click Go, I assume IGV would treat this as 1-based (including the starting base at 100000 and the ending base at 150000). But if IGV loads from a BED file containing this line (chr1 100000 150000), then IGV would include the starting base at 100001 and the ending base at 150000 (not 149999). My understanding comes from this thread (https://tidyomics.com/blog/2018/12/09/2018-12-09-the-devil-0-and-1-coordinate-system-in-genomics/). Please let me know if I am on the right track.

Thank you!
Xiao