anvi-tabulate-trnaseq
Table of Contents
A program to write standardized tab-delimited files of tRNA-seq seed coverage and modification results.
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Authors
Requires
trnaseq-contigs-db 
trnaseq-profile-db
Provides
trnaseq-seed-txt 
modifications-txt
Usage
This program generates tabular files of tRNA-seq seed coverage and modification data that are easily manipulable by the user.
anvi-tabulate-trnaseq is part of the trnaseq-workflow, and is run following the finalization of tRNA seeds by anvi-merge-trnaseq.
This program generates a table, seeds-specific-txt, containing the specific coverage of each nucleotide position in each seed in every sample. If a nonspecific trnaseq-profile-db is also provided, this program generates a table of nonspecific coverages, seeds-non-specific-txt. The distinction between specific and nonspecific coverage is explained in the trnaseq-profile-db artifact. These coverage tables have one row per seed per sample. They have three header rows for different ways of describing tRNA nucleotide positions: canonical position name (e.g., “discriminator_1”), canonical position (e.g., “73”), and “ordinal” position relative to all the other possible positions (e.g., “95”).
anvi-tabulate-trnaseq also generates a table, modifications-txt, containing information on each predicted modification position in each seed, with one row per modification per seed per sample. This table includes four columns of position coverage counts of the four nucleotides.
All tables include taxonomic annotations of the seeds; annotations are added to the trnaseq-contigs-db by anvi-run-trna-taxonomy.
Edit this file to update this information.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-tabulate-trnaseq.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
-c, --contigs-dbCONTIGS_DBrequired- Path to a `trnaseq`-variant contigs database, as produced by `anvi-merge-trnaseq`.
--specific-profile-db, -sPROFILE_DBrequired- The path to an anvi'o profile database containing specific coverage information on tRNA seeds. `anvi-merge-trnaseq` generates a specific profile database from a tRNA-seq experiment.
--nonspecific-profile-db, -nPROFILE_DB- The path to an anvi'o profile database containing nonspecific coverage information on tRNA seeds. `anvi-merge-trnaseq` optionally generates a nonspecific profile database from a tRNA-seq experiment.
-o, --output-dirDIR_PATH- Directory path for output files
-W, --overwrite-output-destinations- Overwrite if the output files and/or directories exist.
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.