output files explanation

[saras224]

Hi @biofuture
I have successfully got the results but I want to know if somewhere you have provided the explanation for the output files generated. I specifically want to know which file should be considered as final outcome? What is the meaning of gene to ppm?

Thanks
Saraswati

[saras224]

Hi @biofuture
I did not get the PCA plot in the output but in the log file it says that it is generating it.
Any Idea why it did not happen?
there is no stage2output.16S.pdf file in the output directory.

Thanks
Saraswati

[biofuture]

Do you have any error message?

[saras224]

Do you have any error message?

no it did not give any error message

[saras224]

hi @biofuture
I got the PCA plots when I had put 3 samples for running the args-oap pipeline, earlier I had put only two samples. But there are two pdfs one is stage2output.16S.pdf and another one is stage2output.cell.pdf. It is comparing the samples with other environment types, are those already present in your database?, can we remove them and compare with our own samples?

Thanks
Saraswati

[biofuture]

Hello, You can use the output 16s subtype table of your own samples to draw PCoA with R. Regards, Xiao-Tao Jiang, Ph.D. Postdoc Research Fellow Microbiome Research Centre St George and Sutherland Clinical School UNSW Sydney Level 2, Clinical Sciences Building (WR Pitney) Short Street, St George Hospital KOGARAH NSW 2217 T: +61 402 943 681 Email: ***@***.******@***.*** MRC web: https://microbiome.org.au/ saras224 ***@***.***> 于2021年8月4日周三 下午4:18写道：

…

hi @biofuture <https://github.com/biofuture> I got the PCA plots when I had put 3 samples for running the args-oap pipeline, earlier I had put only two samples. But there are two pdfs one is stage2output.16S.pdf and another one is stage2output.cell.pdf. It is comparing the samples with other environment types, are those already present in your database?, can we remove them and compare with our own samples? Thanks Saraswati — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#62 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALLDIF23XY5VWSOC4P5RPTT3DLR7ANCNFSM5BIQFAUQ> . 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&utm_campaign=notification-email> .

[saras224]

Thanks @biofuture
you have been very supportive. There is one important thing I wanted to ask is that the output tables have the abundance values in decimals. But what are those abundance values in PPM type table? is it relative abundance of the types and subtypes in percentage or fraction?

[saras224]

Also @biofuture please explain PPM. It is mention that PPM means the number of ARGs sequences in one million sequences?
These one million sequences are my own metagenomics read sequences or one million ARGs sequences in the database?

Saraswati

[biofuture]

Hello, PPM is the part per million which means that number of ARGs reads belong to that ARG subtype per million reads in the metagenomic sample. Regards, Xiao-Tao Jiang, Ph.D. Postdoc Research Fellow Microbiome Research Centre St George and Sutherland Clinical School UNSW Sydney Level 2, Clinical Sciences Building (WR Pitney) Short Street, St George Hospital KOGARAH NSW 2217 T: +61 402 943 681 Email: ***@***.******@***.*** MRC web: https://microbiome.org.au/ saras224 ***@***.***> 于2021年8月9日周一 下午7:07写道：

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Also @biofuture <https://github.com/biofuture> please explain PPM. It is mention that PPM means the number of ARGs sequences in one million sequences? These one million sequences are my own metagenomics read sequences or one million ARGs sequences in the database? Saraswati — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#62 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALLDIE6OU2VFGI2TNUNMGTT36LFLANCNFSM5BIQFAUQ> . 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&utm_campaign=notification-email> .