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Today, I would like to share with you the relevant knowledge points about the method of phenotypic prediction specified by bugbase. The content is detailed and the logic is clear. I believe most people still know too much about this, so share this article for your reference. I hope you can get something after reading this article. Let's take a look at it.

In addition to generating default prediction files of nine phenotypes, Bugbase can also specify phenotypes to predict samples when running locally.

Input file

1. Organize the phenotype you want to predict into a folder in the following format, each file is a phenotype, and the name of the file is the phenotype you want to predict. Here, the five phenotypic files to be predicted are placed in the costom_pathway directory.

The contents of each file are as follows, with one KO ID on one line.

Once the file is ready, run the code.

Run the code

1. Open the DOCKER virtual machine and enter the image (Note: at least 25 GB of memory is required for successful operation, so more memory is needed for docker)

Docker run-- rm-m 25-v D:\ project\ bugbase:/work-it / ampliseq-q1:v1.2

two。 Generate a prediction file of the specified phenotype (the runtime defaults to 16s data)

Make.user.table.r-I costom_pathway/

Parameter description

-I prepare the file directory of the specified phenotype

After running successfully, a process file intermediates (red) and a required specified table row prediction file Custom_BugBase_Traits.txt (yellow) will be produced in the directory.

3. Make phenotypic prediction

Run.bugbase.r-I table.from_txt_json.biom-m fastmap.txt-c loc-u costom_pathway/Custom_BugBase_Traits.txt-o cus_ko

Parameter description

-I otu_table biom1.0 format file (16s must be annotated with GREENGENE database)

-u Forecast file for specified phenotype

-m sample information table

-c specify sample grouping

-o output file name

-t specify classification level 1-7, default door level

-T threshold 0-1, filter threshold can be specified

These are all the contents of this article entitled "methods for bugbase to specify phenotypic prediction". Thank you for reading! I believe you will gain a lot after reading this article. The editor will update different knowledge for you every day. If you want to learn more knowledge, please pay attention to the industry information channel.

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