anvi-convert-trnaseq-database [program]
Table of Contents
A program that processes one or more anvio' tRNA-seq databases generated by anvi-trnaseq to generate anvi'o contigs and merged profile databases that are accessible to the rest of the tools in anvi'o software ecosystem. Briefly, this program will determine final seed sequences from input tRNA-seq databases, determine their coverages across samples, identify tRNA modification sites, and INDELs associated with transcripts in each sample against the seed sequences and store all these data into resulting databases for interactive visualization of the data or in-depth analysis using other anvi'o frameworks.
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Can provide
Can consume
Usage
This program converts one or more trnaseq-dbs into a contigs-db and profile-db, forming tRNA seed sequences in the process.
After anvi-trnaseq is run on a set of samples (or sample splits) from an experiment, the resulting sample databases are analyzed by this program. The contigs-db and profile-db generated by this program can be displayed and analyzed like other ‘omics data in anvi’o.
As with anvi-trnaseq, we encourage you to read through the options in the anvi-convert-trnaseq-database --help menu, since the various analyses occurring within this program can be manipulated by the user. Most of the heavy lifting occurred in anvi-trnaseq, meaning that anvi-convert-trnaseq-database can easily be run multiple times in a matter of minutes to find, for example, the appropriate number of tRNA seed sequences to display (by adjusting --max-reported-trna-seeds) and the necessary coverage cutoffs to isolate positions with modified nucleotides from unfiltered single nucleotide variants (by adjusting --min-third-fourth-nt).
Convert two samples
anvi-convert-trnaseq-database example_trnaseq_database_1 example_trnaseq_database_2 \ -o example_empty_output_directory_path -n example_project_name
Convert two sample splits, assigning priority to the demethylase split in calling the underlying nucleotide at modified positions
anvi-convert-trnaseq-database example_untreated_trnaseq_database example_demethylase_trnaseq_database \ -o example_empty_output_directory_path -n example_project_name --preferred-treatment demethylase
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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.