Getting karyotype file for Candida

[emmannaemeka]

Running Candida_albicans genome UCSC chrom.sizes to get the url did not yield any result to be used. How can I use this tool for a yeast genome not on ucsc browser?

[fomightez]

That script UCSC_chrom_sizes_2_circos_karyotype.py as it is written won't work. However, I just looked at the Candida genome site and if your genomes are there, I can make a separate version of the script that handles their different setup and will give you a karyotype file. I see from here they have Candida albicans SC5314 and WO-1. Would those work? My plan is to modify parts of my script to handle any of the Candida species and strains there. So I'd describe how to determine the exact URL at the Candida genome site to supply the new script and then it would process to give the karyotype file.

[emmannaemeka]

Yes the genome is Candida albicans SC5314 i also have another genome locally assembled i would like to generate karyotype file for.

Can you get a program that can run on locally assembled genome too?

Thanks for your help

On Tue, 21 Jan 2020 at 9:56 PM, fomightez notifications@github.com wrote:

That script UCSC_chrom_sizes_2_circos_karyotype.py https://github.com/fomightez/sequencework/blob/master/circos-utilities/UCSC_chrom_sizes_2_circos_karyotype.py as it is written won't work. However, I just looked at the Candida genome site http://www.candidagenome.org/ and if your genomes are there, I can make a separate version of the script that handles their different setup and will give you a karyotype file. I see from here http://www.candidagenome.org/download/sequence/ they have Candida albicans SC5314 and WO-1. Would those work? My plan is to modify parts of my script to handle any of the Candida species and strains there. So I'd describe how to determine the exact URL at the Candida genome site to supply the new script and then it would process to give the karyotype file.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/fomightez/sequencework/issues/2?email_source=notifications&email_token=AHVLNZ5Y4OYPIYUFD6YJUDTQ65ORTA5CNFSM4KJY6FV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJRHJ3I#issuecomment-576877805, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ7JECB6R2OMGA7VRE3Q65ORTANCNFSM4KJY6FVQ .

-- Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

[fomightez]

A karyotype file for organisms that don't have cytogenetic data is really just a specially formatted list of the chromosomes and the chromosome sizes. You could certainly make a script to make one for a private assembly if that information is fairly parseable from the files. You'd need to share with me names and parts of the files that have that information if you want me to help you with that. My academic email is fairly easy to find if you search my first name, 'Upstate medical' and 'scientist'. My first name is Wayne.

[emmannaemeka]

Thanks email sent.

[emmannaemeka]

Am sure this will help a lot of people

On Tue, 21 Jan 2020 at 9:56 PM, fomightez notifications@github.com wrote:

That script UCSC_chrom_sizes_2_circos_karyotype.py https://github.com/fomightez/sequencework/blob/master/circos-utilities/UCSC_chrom_sizes_2_circos_karyotype.py as it is written won't work. However, I just looked at the Candida genome site http://www.candidagenome.org/ and if your genomes are there, I can make a separate version of the script that handles their different setup and will give you a karyotype file. I see from here http://www.candidagenome.org/download/sequence/ they have Candida albicans SC5314 and WO-1. Would those work? My plan is to modify parts of my script to handle any of the Candida species and strains there. So I'd describe how to determine the exact URL at the Candida genome site to supply the new script and then it would process to give the karyotype file.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/fomightez/sequencework/issues/2?email_source=notifications&email_token=AHVLNZ5Y4OYPIYUFD6YJUDTQ65ORTA5CNFSM4KJY6FV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJRHJ3I#issuecomment-576877805, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ7JECB6R2OMGA7VRE3Q65ORTANCNFSM4KJY6FVQ .

-- Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

[fomightez]

Is the fast you sent me of C. albicans SC5314 A22 the same as at the genome site? Or is that your own assembly?