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

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

ADD COMMENTlink 3.0 years ago Medhat 8.3k • updated 3.0 years ago microfuge ♦ 1.1k
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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 3.0 years ago microfuge ♦ 1.1k
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I tried release 33 but it is empty file

ADD REPLYlink 3.0 years ago
Medhat
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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 3.0 years ago
microfuge
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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 3.0 years ago
Medhat
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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 10 months ago
m.t.lorenc
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