#5 BED off by one projection error.

[Dan Bolser]

BED format is zero based while the chain file is 1-based. This leads to off by one errors when projecting BED.

[Liguo Wang]

This error couldn't happen if your bed and chain files follow the specifications. Could you please provide an example?

[Dan Bolser]

Hi Liguo,

Thanks for getting back to me .

The chain file I'm using is here:
ftp://ftp.ensemblgenomes.org/pub/current/plants/assembly_chain/sorghum_bicolor/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain.gz

Our internal (1-based) database has the following mapping:
V2: 64231291 to 64603896 ->
V3: 71417888 to 71790493

When I use our assembly converter tool (backed by crossmap) to 'see' this mapping using BED format, inputting this works:
1 64231291 64603896

but if I 'properly' 0-base the bed file:
1 64231290 64603895

I get 'no results found'.

[Dan Bolser]

To be honest, I don't know how to read the chain file format. It's possible it's incorrectly representing our 1-based database data.

[Liguo Wang]

Hi,
I can get your region properly mapped using your chain file. Did you use the latest version (0.2.7)?

$ cat test.bed
1 64231290 64603895

$CrossMap.py BED ~/Downloads/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain test.bed
1 64231290 64603895 -> 1 71417887 71790492

the attached chain_to_table.py can print a chain file into a table which is more human readable.