How to create/get cytoband file for Maize (non-model organism) genome

Question

[Medhat]

Hi,

How to create/get cytoband file that I can use with IGV to create .genome file

Answer 1

[microfuge]

Hi cytoband files can be found in ensemble plants ftp dump. For example here ftp://ftp.ensemblgenomes.org/pub/plants/release-25/mysql/zea_mays_core_25_78_6/karyotype.txt.gz I don't know if they have it for the latest AGPV4 release.

[Medhat]

I tried release 33 but it is empty file

[microfuge]

Maybe they don't have it for the latest/newer genome version. Maybe one could download the file for older version (eg AGPV2 ) -> Convert to bed -> use crossmap/liftover to get the new version coordinates ?

[Medhat]

the new version had a lot of upgrades I do not think lifting over is a good solution , besides I tried to lift over a vcf file and it did not work well

[m.t.lorenc]

I found here is a description of the file format. I can write a script which gets the first 3 columns values out samtools faidx output. Does anyone know how to determine the last 2 columns (name and gieStain)?