Closed liamxg closed 2 months ago
koppk
commented
1 year ago Hi Liam, Nextstrain_clade is a column header if you download metadata "as for input in Augur pipeline" from GISAID (not "as sequencing technology metadata"). Often you will find a "?" but you could replace that with values you might generate yourself by running the corresponding fasta sequences through Nextclade (standalone or webserver-based: https://clades.nextstrain.org/). Cheers, Katharina
jsan4christ
commented
1 year ago Yes that's correct. Sorry for some reason I thought the two of you were the same person.
On Sun, Oct 9, 2022, 4:37 AM Liam @.***> wrote:
@koppk https://github.com/koppk thanks for your help. many analysis is not familiar to me, hope you can help me on this.
— Reply to this email directly, view it on GitHub https://github.com/CERI-KRISP/SARS-CoV-2-epidemic-in-Africa/issues/2#issuecomment-1272437857, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGBQRTKMVOFBD53V5MD5L3WCIVVDANCNFSM6AAAAAAQP3AF7I . You are receiving this because you were mentioned.Message ID: @.***>
jsan4christ
commented
1 year ago That would be against the GISAID T&C but I will create an EPI_SET ID and share here.
On Sun, Oct 9, 2022 at 11:27 AM Liam @.***> wrote:
@jsan4christ https://github.com/jsan4christ can you share the meta data file for me, thanks.
— Reply to this email directly, view it on GitHub https://github.com/CERI-KRISP/SARS-CoV-2-epidemic-in-Africa/issues/2#issuecomment-1272499145, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGBQRT222ZRL5TGNMSIJODWCKFX7ANCNFSM6AAAAAAQP3AF7I . You are receiving this because you were mentioned.Message ID: @.***>
The Lord is my shepherd, I shall not want! Psalms 23
jsan4christ
commented
1 year ago Correct, but here is the Epi set;
EPI_SET ID: | EPI_SET_221009wd doi: | 10.55876/gis8.221009wd
EPI_SET ID: EPI_SET_221009wd
doi: 10.55876/gis8.221009wd
jsan4christ
commented
1 year ago Hi Liam,
I believe that is a field you derive. You can generate by running the sequences through Nextclade and merging that field. The Nextstrain team keep changing the format of their output by dropping or renaming some fields and adding others. Sometimes we also add or derive depending on the needs of the analysis.
On Thu, Sep 22, 2022 at 4:57 AM Liam @.***> wrote:
@jsan4christ https://github.com/jsan4christ can not find Nextstrain_clade in Fig1.R.
— Reply to this email directly, view it on GitHub https://github.com/CERI-KRISP/SARS-CoV-2-epidemic-in-Africa/issues/2#issuecomment-1254455248, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGBQRVW5TAJNTKLQGVFMZLV7PDJLANCNFSM6AAAAAAQP3AF7I . You are receiving this because you were mentioned.Message ID: @.***>
The Lord is my shepherd, I shall not want! Psalms 23
jsan4christ
commented
1 year ago No problem,
Any time.
On Tue, Oct 11, 2022 at 10:15 AM Liam @.***> wrote:
@jsan4christ https://github.com/jsan4christ thanks for your help.
— Reply to this email directly, view it on GitHub https://github.com/CERI-KRISP/SARS-CoV-2-epidemic-in-Africa/issues/2#issuecomment-1274283054, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGBQRWS3CIMYKWMYWJ7AADWCUO3PANCNFSM6AAAAAAQP3AF7I . You are receiving this because you were mentioned.Message ID: @.***>
The Lord is my shepherd, I shall not want! Psalms 23
jsan4christ
commented
1 year ago @.***
On Tue, Oct 11, 2022 at 10:29 AM Liam @.***> wrote:
@jsan4christ https://github.com/jsan4christ can I get your email, for cooperation?
— Reply to this email directly, view it on GitHub https://github.com/CERI-KRISP/SARS-CoV-2-epidemic-in-Africa/issues/2#issuecomment-1274302474, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGBQRVD4IPTWMW7WVCQZ73WCUQNJANCNFSM6AAAAAAQP3AF7I . You are receiving this because you were mentioned.Message ID: @.***>
The Lord is my shepherd, I shall not want! Psalms 23
Hi Liam,
This is GISAID metadata, the policy does not allow sharing it directly, one has to get the ids and download from GISAID after accepting the user policy. Also this file is particularly large, i.e. great than 100M so cannot be uploaded to a standard GitHub repo.