mbtools guide

[Fla1487]

There is a mbtools guide to use completely the package? i.e. similar to phyloseq guide? Thanks a lot

[cdiener]

Is https://gibbons-lab.github.io/mbtools/ what you are looking for? The Articles section covers most of the package.

[Fla1487]

Thank you so much for replaying.

I am interested in using mbtools for 16s data analysis, like I have seen on a recent paper that you have published. I do not understand two main step: a) removing primers or not biologic sequences (in qiime2 2 is before DADA2 alghoritm); b) assigning taxnomy.

Thank you in advance Flavio

Inviato da Postahttps://go.microsoft.com/fwlink/?LinkId=550986 per Windows

Da: Christian @.> Inviato: mercoledì 13 ottobre 2021 22:44 A: @.> Cc: De Maio @.>; @.> Oggetto: Re: [Gibbons-Lab/mbtools] mbtools guide (#3)

Is https://gibbons-lab.github.io/mbtools/https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgibbons-lab.github.io%2Fmbtools%2F&data=04%7C01%7Cflavio.demaio%40unicatt.it%7Cd8c2a9f5b4b949b12af208d98e8a3a60%7Cb94f7d7481ff44a9b5886682acc85779%7C0%7C0%7C637697546598841766%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Y4jVM7S4GA3W8R%2F1C0fhEXFjpqwJ7iPsZdxfMG5lNXs%3D&reserved=0 what you are looking for? The Articles section covers most of the package.

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[cdiener]

Sorry for the delay. mbtools starts with demultiplexed data (like the ones you get from Illumina basespace), so those should already have the primers removed. You could preprocess your read files with cutadapt or some other tool if you haver additional non-biological sequences in there. The preprocessing also has an entropy plot that can be used to check if you still have adapter sequences (if most of your reads have adapter sequences you will observe very low, <0.05, entropy on the 5' end). If that is the case you could also just adjust the trimLeft parameter to cut them off. Taxonomy assignment is included in the denoise step and you can specify the database in the config. If you don't specify anything it will use SILVA 138.1 for the taxonomy assignment.

[Fla1487]

Thank you so much for your information. I had this idea about pre-processing, but generally most people prefer performing demultiplexing and then trimming…Fantastic information!

I will try mbtools and I will wirte, if possible, for additional questions.

Thank you so much again

F

Inviato da Postahttps://go.microsoft.com/fwlink/?LinkId=550986 per Windows

Da: Christian @.> Inviato: lunedì 18 ottobre 2021 20:48 A: @.> Cc: De Maio @.>; @.> Oggetto: Re: [Gibbons-Lab/mbtools] mbtools guide (#3)

Sorry for the delay. mbtools starts with demultiplexed data (like the ones you get from Illumina basespace), so those should already have the primers removed. You could preprocess your read files with cutadapt or some other tool if you haver additional non-biological sequences in there. The preprocessing also has an entropy plot that can be used to check if you still have adapter sequences (if most of your reads have adapter sequences you will observe very low, <0.05, entropy on the 5' end). If that is the case you could also just adjust the trimLeft parameter to cut them off. Taxonomy assignment is included in the denoise step and you can specify the database in the config. If you don't specify anything it will use SILVA 138.1 for the taxonomy assignment.

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[cdiener]

Awesome, good luck :smile: