anvi-export-gene-coverage-and-detection

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Export gene coverage and detection data for all genes associated with contigs described in a profile database.

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Requires

profile-db contigs-db

Can use

genes-of-interest-txt

Provides

coverages-txt detection-txt

Usage

This program gives you the coverage and detection data for all of the genes found in your contigs-db, using the short reads data in your profile-db.

anvi-export-gene-coverage-and-detection -c contigs-db \ -p profile-db \ -O MY_DATA

This will give you a coverages-txt and a detection-txt whose file names will begin with MY_DATA

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-export-gene-coverage-and-detection.

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

anvi-export-gene-coverage-and-detection [-h] -p PROFILE_DB -c CONTIGS_DB -O FILENAME_PREFIX [--gene-caller-id GENE_CALLER_ID] [--genes-of-interest FILE]

Parameters and their descriptions

DATABASES Anvi'o databases to read from

-p, --profile-db PROFILE_DB required: Anvi'o profile database
-c, --contigs-db CONTIGS_DB required: Anvi'o contigs database generated by 'anvi-gen-contigs-database'

OUTPUT Define a prefix for your output files

-O, --output-file-prefix FILENAME_PREFIX required: A prefix to be used while naming the output files. No file type extensions please; just a prefix -- all ouptut file names and extensions will be appended to this prefix.

GENES Gene calls you want to work with. Without these parameters anvi'o will report everything it finds in the profile database (please) note that the reported genes will only include those that occur in contigs that were taken into consideration during `anvi-profile`, which means if there was a length cutoff for profiling, genes that occur in contigs shorter than that cutoff will not appear in your output.

--gene-caller-id GENE_CALLER_ID: A single gene id.
--genes-of-interest FILE: A file with anvi'o gene caller IDs. There should be only one column in the file, and each line should correspond to a unique gene caller id (without a column header).

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.