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B-UMMI / chewBBACA

BSR-Based Allele Calling Algorithm
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How to find cgMLST of Staphylococcus pseudintermedius #111

Closed sekhwal closed 4 months ago

sekhwal commented 2 years ago

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

ramirma commented 2 years ago

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. Do not hesitate to contact us again if we can help with anything else. Mario

sekhwal commented 2 years ago

Hi,

I installed chewBBACA using conda and followed all the steps of the following tutorials. https://github.com/B-UMMI/chewBBACA https://github.com/B-UMMI/chewBBACA_tutorial

I have got several output files such as (.protein.fasta, cgMLST.tsv, results_alleles.tsv, Genes_95%.txt).

Now, I have follow up questions. 1). How I can get cgMLST of my assembly genomes. I tried to find in the output files but the files contain a very large data but no cgMLST. 2). Once I am using the following command, it shows following error:

chewBBACA.py JoinProfiles -p1 /cgMLST_95/cgMLST.tsv -p2 /results_alleles.tsv -o cgMLST_all.tsv

---------error----------- JoinProfiles: error: unrecognized arguments: Staph_cgMLST/cgMLST/cgMLST.tsv Staph_cgMLST/Staph_AlleleCall/results_alleles.tsv

Thank you!!

sekhwal commented 2 years ago

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!

sekhwal commented 2 years ago

Hi, Please let me know how to proceed to identify cgMLST next after getting the schema of "Staphylococcus pseudintermedius".

cimendes commented 2 years ago

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 chewBBACA.py ExtractCgMLST module. More information is also available in chewBBACA's wiki

cimendes commented 2 years ago

I have got several output files such as (.protein.fasta, cgMLST.tsv, results_alleles.tsv, Genes_95%.txt).

cgMLST.tsv should contain your cgMLST profile, which you can visualize in phyloviz online

sekhwal commented 2 years ago

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.

ramirma commented 2 years ago

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

sekhwal commented 2 years ago

Thank you for your reply. I sent an email at @.*** .

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

— Reply to this email directly, view it on GitHub https://github.com/B-UMMI/chewBBACA/issues/111#issuecomment-1024345141, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGHR4LTI7RWHUDNT3UOLKPDUYK27LANCNFSM5MH3HQ2Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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sekhwal commented 2 years ago

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. Thank you, Manoj

ireneortega commented 2 years ago

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.

ramirma commented 1 year ago

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.

rfm-targa commented 4 months ago

Closing this issue. chewBBACA does not include a module to determine cgSTs, but the allele calling results can be analysed with other tools to get to that point. We added some suggestions in another issue's comments here.