Microbial 'omics


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pn-ps-data [artifact]

Table of Contents

CONCEPT

A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

Back to the main page of anvi’o programs and artifacts.

Provided by

anvi-script-calculate-pn-ps-ratio

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

This describes the output of anvi-script-calculate-pn-ps-ratio, which calculates the pN/pS ratio for each gene in a contigs-db.

See the page for anvi-script-calculate-pn-ps-ratio for an explanation of the pN/pS ratio

This describes a directory that contains the following three files:

pN_pS_ratio.txt: a matrix of the pN/pS values where each row is a gene and each column is a metagenome.

gene_caller_id  ANE_004_05M             ANE_004_05M             ANE_150_05M           ...
1248            0.024404785965479868    0.024404785965479868    0.019650249960943812
1249            0.014399205561072536    0.014399205561072536    0.0
...

SAAV_counts.txt: a matrix that describes the number of SAAVs for each gene in each metagenome.

gene_caller_id  ANE_004_05M     ANE_004_05M     ANE_150_05M      ...
1248            12              11              10    
1249            1               1               0
...

SCV_counts.txt: a matrix that describes the number of SCVs for each gene in each metagenome.

gene_caller_id  ANE_004_05M     ANE_004_05M     ANE_150_05M      ...
1248            143             154             148    
1249            19              19              14
...

Edit this file to update this information.