Running Pipeline Favour

[helena-shapton]

Hi Alex,

I have the remaining plate sequences now and I'm really intrigued to see the results Re: your meeting with Jim yesterday. I have tried to contact Jim and Laura all day to assist but no luck so could you possibly run the following and send me all the outputs (inc. raw OTU cluster fasta for all sequences). Zip file is being a pain and not uploading so I have sent to your gmail. Also I a different file tag and output folder but I still couldn't get the sequences to assemble.

Helena

[blex-max]

Sure - can you send me a zip with all the traces you want done, including ones I've done for you before?

…

On Thu, May 12, 2022 at 4:08 PM helena-shapton ***@***.***> wrote: Hi Alex, I have the remaining plate sequences now and I'm really intrigued to see the results Re: your meeting with Jim yesterday. I have tried to contact Jim and Laura all day to assist but no luck so could you possibly run the following and send me all the outputs (inc. raw OTU cluster fasta for all sequences). Zip file is being a pain and not uploading so I have sent to your gmail. Also I a different file tag and output folder but I still couldn't get the sequences to assemble. Helena — Reply to this email directly, view it on GitHub <#18>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APSXEGODIZ7X7SOYFST6H53VJUNGHANCNFSM5VYST6QQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[helena-shapton]

Sent to both of your emails it won't attach on git for some reason

[helena-shapton]

Shapton, Helena has shared a OneDrive for Business file with you. To view it, click the link below. <https://imperiallondon-my.sharepoint.com/personal/hs1019_ic_ac_uk/Documents/Attachments/ITS_sequences%205.zip> [https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]<https://imperiallondon-my.sharepoint.com/personal/hs1019_ic_ac_uk/Documents/Attachments/ITS_sequences%205.zip> ITS_sequences 5.zip<https://imperiallondon-my.sharepoint.com/personal/hs1019_ic_ac_uk/Documents/Attachments/ITS_sequences%205.zip> Helena Shapton Final Year Biological Sciences Imperial College London South Kensington Campus London SW7 2AZ, UK Tel: (+44) 07891 668811

________________________________ From: blex-max ***@***.***> Sent: 12 May 2022 16:28 To: kew-myco/its_glue ***@***.***> Cc: Shapton, Helena ***@***.***>; Author ***@***.***> Subject: Re: [kew-myco/its_glue] Running Pipeline Favour (Discussion #18) This email from ***@***.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Sure - can you send me a zip with all the traces you want done, including ones I've done for you before?

On Thu, May 12, 2022 at 4:08 PM helena-shapton ***@***.***> wrote: Hi Alex, I have the remaining plate sequences now and I'm really intrigued to see the results Re: your meeting with Jim yesterday. I have tried to contact Jim and Laura all day to assist but no luck so could you possibly run the following and send me all the outputs (inc. raw OTU cluster fasta for all sequences). Zip file is being a pain and not uploading so I have sent to your gmail. Also I a different file tag and output folder but I still couldn't get the sequences to assemble. Helena — Reply to this email directly, view it on GitHub <#18>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APSXEGODIZ7X7SOYFST6H53VJUNGHANCNFSM5VYST6QQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub<#18 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AP2JM3MOUDJTDGIULAHSW3LVJUPSNANCNFSM5VYST6QQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[helena-shapton]

To view ITS_sequences 5.zip, sign in<https://imperiallondon-my.sharepoint.com/personal/hs1019_ic_ac_uk/_layouts/15/acceptinvite.aspx?invitation=%7B39658DD6%2D45A1%2D4609%2D9CA3%2DE5C13B8FE736%7D&listId=245f8dc6%2D8cff%2D42f0%2Daf1b%2D8c7486e6da82&itemId=b431377f%2Df81a%2D473c%2Da248%2D671d9f6a22f5> or create an account.

[blex-max]

I can't access any of those - can you send it as a google drive link to my gmail perhaps?

[helena-shapton]

Sent

[helena-shapton]

Any updates?

[blex-max]

Done

helena.15_05_22.zip

[helena-shapton]

Thank you If possible, Laura also believes there to be a file available that assigns an SH number to all OTUs which could be usful to use? Helena Shapton Final Year Biological Sciences Imperial College London South Kensington Campus London SW7 2AZ, UK Tel: (+44) 07891 668811

…

________________________________ From: blex-max ***@***.***> Sent: 15 May 2022 14:41 To: kew-myco/its_glue ***@***.***> Cc: Shapton, Helena ***@***.***>; Author ***@***.***> Subject: Re: [kew-myco/its_glue] Running Pipeline Favour (Discussion #18) This email from ***@***.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Done helena.15_05_22.zip<https://github.com/kew-myco/its_glue/files/8695057/helena.15_05_22.zip> — Reply to this email directly, view it on GitHub<#18 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AP2JM3L65Q5WA6CFGCQ2FLLVKD5JPANCNFSM5VYST6QQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[blex-max]

That file doesn't strictly exist the way you've put it, but there is a file of attempted sintax classifications for every sequence, including best matches below the sintax cutoff to accept as 'true'. I think this is probably what you mean, so attached. Tab-separated values. If you needed to match these to clusters, you can use this in combo with the cluster membership table. But a quick warning: Using below-cutoff matches entirely defeats the point of taxonomy assignment algorithm with taxonomic-rank confidence scores. You will introduce a lot of over-classification errors.
sintax_classifications.tsv