Microbial 'omics


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anvi-trnaseq [program]

Table of Contents

A program to process reads from a tRNA-seq dataset to generate an anvi'o tRNA-seq database.

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Authors

Can consume

trnaseq-fasta

Can provide

trnaseq-db

Usage

This program analyzes a tRNA-seq library, generating de novo predictions of tRNA sequences, structures, and modification positions.

A FASTA file of merged paired-end tRNA-seq reads is required as input. This file is produced by the initial steps of the trnaseq-workflow, in which Illumina-utils, merges paired-end reads and anvi-script-reformat-fasta creates anvi’o-compliant deflines in the FASTA file.

The primary output of anvi-trnaseq is a trnaseq-db. Supplemental outputs are also produced – an analysis summary, a tabular file of unique sequences not identified as tRNA, an a tabular file of 5’ and 3’ extensions trimmed off mature tRNA.

The anvi-trnaseq --help menu provides detailed explanations of the parameters controlling the multifacted analyses performed by the program.

Examples

Generate a trnaseq-db from a sample using 16 cores.

anvi-trnaseq -f trnaseq-fasta \ -S SAMPLE_NAME \ -o OUTPUT_DIRECTORY \ -T 16

Generate a trnaseq-db from a sample flagged as being treated with demethylase. The output directory is overwritten if it already exists.

anvi-trnaseq -f trnaseq-fasta \ -S SAMPLE_NAME \ -o OUTPUT_DIRECTORY \ -T 16 \ --treatment demethylase \ --overwrite-output-destinations

Parameterize tRNA feature profiling

Feature profiling parameters can be modified by the user by in an optional .ini file. For example, the user may want a more permissive definition of a tRNA (more false positive identifications of sequences as tRNA, fewer false negative failures to identify sequences as tRNA), increasing the number of unpaired nucleotides allowed in the T stem or increasing the number of unconserved canonical nucleotides allowed in the anticodon loop. Numerous structural parameters like these can be altered.

Write the .ini file to param.ini.

anvi-trnaseq --default-feature-param-file PARAM.ini

Nicely display the .ini defaults that can be written to the file in standard output.

anvi-trnaseq --print-default-feature-params

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.