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classification using database #23

Open laibinhuang opened 2 years ago

laibinhuang commented 2 years ago

It is possible to get the classification for some interesting functional genes:

I want to know both the abundance and the classification for AOA, AOB, nirK/S and nosZ; wonder how can I do this using this database and pipeline.

thank you

qichao1984 commented 2 years ago

Hello, taxonomic assignment using NCycDB is not recommended. However, I would suggest you to use our recently developed script (SCycDB_TaxonomyProfiler.PLhttps://github.com/qichao1984/SCycDB/blob/master/SCycDB_TaxonomyProfiler.PL) in SCycDB (GitHub - qichao1984/SCycDBhttps://github.com/qichao1984/SCycDB) for taxonomic assignment. The script employs seqtk to extract targeted N cycling sequences and make taxonomic assignment using Kraken2. You may need to make some revisions to make it work with NCycDB, but it should be relatively easy. Sorry that I myself am too busy working on many issues, otherwise I can do it.

发件人: @.> 发送时间: 2021年12月9日 2:25 收件人: @.> 抄送: @.***> 主题: [qichao1984/NCyc] classification using database (Issue #23)

It is possible to get the classification for some interesting functional genes:

I want to know both the abundance and the classification for AOA, AOB, nirK/S and nosZ; wonder how can I do this using this database and pipeline.

thank you

― You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/qichao1984/NCyc/issues/23, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABNORGA3ZZAGF7OEGJ4IEYLUP6PK7ANCNFSM5JUPDWGQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

laibinhuang commented 2 years ago

thank you,

do you mean I can do this by changing:

(1) id2gene.2020Mar.map to id2gene.map.2019Jul in the SCycDB_TaxonomyProfiler.PL script (2)SCycDB_2020Mar to NCyc_100_2019Jul.7z in the SCycDB_TaxonomyProfiler.PL script

and then replace them in the package of SCycdB,

Thank you again!

laibinhuang commented 2 years ago

Dear professor Tu,

Please let me know I am in the correct way and give a little bit more details on the modification, thank you very much! I am doing nitrogen cycling a lot, but not very familiar the bioinformatics.

Best, Laibin

qichao1984 commented 2 years ago

Laibin, This should be OK! However, you may encounter issues related with seqtk and kraken2, or something else. Some details can not be expected without thoroughly debugging the script. I encourage you to test the script after modification. Otherwise it is hard to figure out those potential issues. All in all, the basic idea is to extract targeted sequences, and do taxonomic assignment using third party tools.

发件人: @.> 发送时间: 2021年12月14日 13:59 收件人: @.> 抄送: Qichao @.>; @.> 主题: Re: [qichao1984/NCyc] classification using database (Issue #23)

Dear professor Tu,

Please let me know I am in the correct way and give a little bit more details on the modification, thank you very much! I am doing nitrogen cycling a lot, but not very familiar the bioinformatics.

Best, Laibin

― You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/qichao1984/NCyc/issues/23#issuecomment-993185569, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABNORGC6THMYS3EES5NBSYTUQ3MMVANCNFSM5JUPDWGQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

laibinhuang commented 2 years ago

sure, thank you!

Laibin

On Mon, Dec 13, 2021 at 11:32 PM Qichao Tu @.***> wrote:

Laibin, This should be OK! However, you may encounter issues related with seqtk and kraken2, or something else. Some details can not be expected without thoroughly debugging the script. I encourage you to test the script after modification. Otherwise it is hard to figure out those potential issues. All in all, the basic idea is to extract targeted sequences, and do taxonomic assignment using third party tools.

发件人: @.> 发送时间: 2021年12月14日 13:59 收件人: @.> 抄送: Qichao @.>; @.> 主题: Re: [qichao1984/NCyc] classification using database (Issue #23)

Dear professor Tu,

Please let me know I am in the correct way and give a little bit more details on the modification, thank you very much! I am doing nitrogen cycling a lot, but not very familiar the bioinformatics.

Best, Laibin

― You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/qichao1984/NCyc/issues/23#issuecomment-993185569>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ABNORGC6THMYS3EES5NBSYTUQ3MMVANCNFSM5JUPDWGQ>.

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>.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/qichao1984/NCyc/issues/23#issuecomment-993238430, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU52BTLI43FZFYPOD73UQ3XKLANCNFSM5JUPDWGQ . 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.

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

University of California - Davis Department of Land, Air, and Water Resources Soil EcoGenomics Lab - @SEcoGenomics Plant and Environmental Sciences Building Room 3307 Davis, CA 95616 USA Email: @.***