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How to find cgMLST of Staphylococcus pseudintermedius #111
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Dear Manoj, Sorry for not having responded sooner. If you are asking if there is already a publicly available schema for Staphylococcus pseudintermedius in chewie-NS there is no such schema. If you want to develop one, you can use chewBBACA to do so. I would suggest you look at the wiki pages. |
Hi, I installed chewBBACA using conda and followed all the steps of the following tutorials. I have got several output files such as (.protein.fasta, cgMLST.tsv, results_alleles.tsv, Genes_95%.txt). Now, I have follow up questions. ##chewBBACA.py JoinProfiles -p1 /cgMLST_95/cgMLST.tsv -p2 /results_alleles.tsv -o cgMLST_all.tsv Thank you!! |
I have created a cgMLST schema for "Staphylococcus pseudintermedius" using chewBBACA, please let me know how to proceed to get cgMLST of my assembled genomes. Thank you! |
Hi, Please let me know how to proceed to identify cgMLST next after getting the schema of "Staphylococcus pseudintermedius". |
Hello On the cgMLST schema determination of the chewBBACA tutorial repository, you have the information on how to extract the cgMLST from a schema. You'll be using |
cgMLST.tsv should contain your cgMLST profile, which you can visualize in phyloviz online |
Yes, I got the cgMLST from the schema using chewBBACA.py ExtractCgMLST but I am not sure where the cgMLST number. For instance, scaffold1.fasta belongs to 1252cgMLST. However, in the results of chewBBACa, the excel file contains large datasets. |
Dear Manoj, I am not sure I understand what you mean. Could you send us the output files you got? If you prefer you can email us at imm-bioinfo@medicina.ulisboa.pt. Mario |
Thank you for your reply. I sent an email at ***@***.***
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Manoj
…On Fri, Jan 28, 2022 at 10:47 AM ramirma ***@***.***> wrote:
Dear Manoj,
I am not sure I understand what you mean. Could you send us the output
files you got? If you prefer you can email us at
***@***.***
Mario
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Hi, please let me know if there is any update about my query. Still I am trying to understand how to get cgST from the Schemes. I may not be correct to understand the way. Any clarification would be highly appreciated. |
I think @sekhwal wants to get the number for the cgST, that is a single value from the cgMLST chema. For example, the ST is obtained from the seven MLST loci. So, cgST would be similarly obtained from the cgMLST chema. I am also interested in this. For example, in pubmlst.org you can get the the closest profile cgST when selecting cgMLST chema. |
Sorry, the issue was left dangling. chewBBACA does not provide a unique identifier or ST number for a given cgMLST profile. This is a difficult problem for which we do not have a solution currently implemented. |
I am using chewBBACA for identifying cgMLST of species Staphylococcus pseudintermedius. Please let me know if I am able to get it using the database to get the cgMLST information of the species.
Thank you,
Manoj
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