Question: How to create/get cytoband file for Maize (non-model organism) genome
0
gravatar for Medhat
3.7 years ago by
Medhat8.8k
Texas
Medhat8.8k wrote:

Hi,

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

sequencing • 1.7k views
ADD COMMENTlink modified 3.7 years ago by microfuge1.9k • written 3.7 years ago by Medhat8.8k
2
gravatar for microfuge
3.7 years ago by
microfuge1.9k
microfuge1.9k wrote:

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.

ADD COMMENTlink written 3.7 years ago by microfuge1.9k

I tried release 33 but it is empty file

ADD REPLYlink written 3.7 years ago by Medhat8.8k

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 ?

ADD REPLYlink written 3.7 years ago by microfuge1.9k

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

ADD REPLYlink written 3.7 years ago by Medhat8.8k

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)?

ADD REPLYlink modified 20 months ago • written 20 months ago by m.t.lorenc0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2109 users visited in the last hour