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MDU-PHL / COVID19-paper

Data for publications related to Victorian SARS-CoV-2 genomic epidemiology
GNU General Public License v3.0
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could you please share the corresponding GISAID ids? #2

Closed anwarMZ closed 3 years ago

anwarMZ commented 3 years ago

Hi, I am really interested in your article & dataset. Could you please share the corresponding GISAID genome IDs for the bioSamples ? If the file cant be shared here you can use my email too. email: zohaib_anwar@ymail.com

Thanks, Zohaib

andersgs commented 3 years ago

@anwarMZ the GISAID IDs are in the BioSample description field: https://www.ncbi.nlm.nih.gov/biosample/16975848

Best. Anders.

anwarMZ commented 3 years ago

Thank you very much @andersgs I just wanted to make sure that the IDS are updated or resolved with GISAID? As mentioned in README.md that some of them had an issue due to "frame shift"?

andersgs commented 3 years ago

That is correct. Not all were accepted by GISAID. There is nothing we can do about those, unfortunately.

A.

From: Muhammad Zohaib Anwar notifications@github.com Reply-To: MDU-PHL/COVID19-paper reply@reply.github.com Date: Monday, January 18, 2021 at 11:30 AM To: MDU-PHL/COVID19-paper COVID19-paper@noreply.github.com Cc: Anders Gonçalves da Silva andersgs@gmail.com, Mention mention@noreply.github.com Subject: Re: [MDU-PHL/COVID19-paper] could you please share the corresponding GISAID ids? (#2)

Thank you very much @andersgshttps://github.com/andersgs I just wanted to make sure that the IDS are updated or resolved with GISAID? As mentioned in README.mdhttps://github.com/MDU-PHL/COVID19-paper#consensus-genomes that some of them had an issue due to "frame shift"?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/MDU-PHL/COVID19-paper/issues/2#issuecomment-762434995, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA5IVOY2AT5XIWXGY52ZZJTS2SD67ANCNFSM4WGVD6EQ.

anwarMZ commented 3 years ago

fair enough, but do you have a list GISAID ids of those that were accepted separately? This will just make it more straightforward to fetch them directly from GISAID. If not I believe I will have to run a search through and see which one's are in GISAID, right?

andersgs commented 3 years ago

I have asked our data manager to generate a table, and will upload soon. Please see issue #3.

A.

From: Muhammad Zohaib Anwar notifications@github.com Reply-To: MDU-PHL/COVID19-paper reply@reply.github.com Date: Monday, January 18, 2021 at 12:02 PM To: MDU-PHL/COVID19-paper COVID19-paper@noreply.github.com Cc: Anders Gonçalves da Silva andersgs@gmail.com, Mention mention@noreply.github.com Subject: Re: [MDU-PHL/COVID19-paper] could you please share the corresponding GISAID ids? (#2)

fair enough, but do you have a list GISAID ids of those that were accepted separately? This will just make it more straightforward to fetch them directly from GISAID. If not I believe I will have to run a search through and see which one's are in GISAID, right?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/MDU-PHL/COVID19-paper/issues/2#issuecomment-762446908, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA5IVOZKXD2YGX22OLMKDTDS2SHVPANCNFSM4WGVD6EQ.

anwarMZ commented 3 years ago

Fantastic. Thank you @andersgs !