Documentation Issues

[elsamdea]

Hi!

I was reading the documentation and following the sections steps when I saw some typos:

Inside the "Sequence Reconstruction" Section:

In the alignment folder:

• There is not a "green-lantern" file. Instead, there is a "region3" file.

In the documentation:

• In the alignment step, the green-lantern command fails. It is because the command is described as:

qiime sidle align-regional-kmers
--i-kmers alignment/green-lantern-kmer-db.qza
--i-rep-seq table/green-lantern-rep-seq.qza
--p-region GreenLantern
--p-n-workers 2
--o-regional-alignment alignment/green-lantern-align-map.qza

But it is should be:

qiime sidle align-regional-kmers
--i-kmers database/sidle-db-green-lantern-100nt-kmers.qza
--i-rep-seq data/green-lantern-100nt-rep-set.qza
--p-region GreenLantern
--p-n-workers 2
--o-regional-alignment alignment/green-lantern-align-map.qza

Also, I was wondering where I built the "aligned-sequence-database based file" used in the "Phylogenetic Reconstruction" inside the "Sequence Reconstruction" Section.

Regards,

Elsa

[jwdebelius]

Hi @elsamdea,

Sorry for the long follow up. I think this is fixed in the updated branch (#27). But, I'm waiting for a review. Thank you and i'll keep you updated!

I will try to make sure the database sources are better described and may ask you if you're willing to review when we hit that point, if you're comfortable.

[elsamdea]

Hi @jwdebelius, (I answer by email because I can't find the place to do it on github). Don't worry, I understand there is so much on the way. Also, I take advantage of this email to comment that, in *the phylogeny step*, if the command fails with *the error "conda libraries deprecating method ".iloc()",* you can add that a solution is to update directly in terminal with the command "*conda panda updates"*. (I can open an issue if you wish). It will be an honor to review! And, if there is another way to help, please let me know :). Best regards, Elsa

…

On Mon, 20 Sept 2021 at 17:25, Justine Debelius ***@***.***> wrote: Hi @elsamdea <https://github.com/elsamdea>, Sorry for the long follow up. I *think* this is fixed in the updated branch (#27 <#27>). But, I'm waiting for a review. Thank you and i'll keep you updated! I will try to make sure the database sources are better described and may ask you if you're willing to review when we hit that point, if you're comfortable. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK6LCP4TR26FZD2WS4VHDNTUC5G5VANCNFSM5DD2ZRXQ> . 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>.