anvi-gen-gene-level-stats-databases

Authors
Requires
Can use
Provides
Usage

Other Parameters

Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

A program to compute genes databases for a ginen set of bins stored in an anvi'o collection. Genes databases store gene-level coverage and detection statistics, and they are usually computed and generated automatically when they are required (such as running anvi-interactive with --gene-mode flag). This program allows you to pre-compute them if you don't want them to be done all at once.

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

Authors

A. Murat Eren (Meren)

Requires

profile-db contigs-db

Can use

collection bin

Provides

genes-db

Usage

This program generates a genes-db, which stores the coverage and detection values for all of the genes in your contigs-db.

This information is usually calculated when it’s needed (for example when running anvi-interactive in genes mode), but this program lets you break this process into two steps. This way, you can easily change the parameters of anvi-interactive without having to recalculate the gene-level statistics.

Given a contigs-db and profile-db pair, as well as a collection, this program will calculate the stats for the genes in each of your bins and give each bin its own profile-db that includes this information.

For example, if a collection called GENE_COLLECTION contained the bins bin_0001, bin_0002, and bin_0003 and you ran:

anvi-gen-gene-level-stats-databases -c contigs-db \ -p profile-db \ -C collection

Then it will create a directory called GENES that contains three profile-db called GENE_COLLECTION-bin_0001.db, GENE_COLLECTION-bin_0002.db, and GENE_COLLECTION-bin_0003.db. In terms of output, this program is similar to anvi-split: each of these databases can now be treated as self-contained anvi’o projects but they also contain the gene-level information. Thus, you then could run anvi-interactive in genes mode on one of these profile databases.

You also have the option to provide a list of bin (either as a file or as a string) to anlyze instead of a single collection.

Other Parameters

You can also change the definition of an outlier nucleotide position or switch calculations to use the INSeq/Tn-Seq statistical methods.

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-gen-gene-level-stats-databases.

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-gen-gene-level-stats-databases [-h] -c CONTIGS_DB -p PROFILE_DB [-C COLLECTION_NAME] [-b BIN_NAME] [-B FILE_PATH] [--zeros-are-outliers] [--outliers-threshold NUM] [--just-do-it] [--inseq-stats]

Parameters and their descriptions

INPUT DATABASES Which anvi'o databases do you wish to work today?

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

BIN(S) AND COLLECTION You can select a bin, multiple bins, or you can simply focus on every bin in a collection by providing only a collection name. Once you are done with your selection, anvi'o will generate an individual genes database for each of the bin it finds.

-C, --collection-name COLLECTION_NAME: Collection name.
-b, --bin-id BIN_NAME: Bin name you are interested in.
-B, --bin-ids-file FILE_PATH: Text file for bins (each line should be a unique bin id).

ADDITIONAL PARAMETERS These parameters are those that are critical to identify outlier nucleotide positions and how to define what should be included in those calculations. In most cases you can leave them as is, and things are going to be alright.

--zeros-are-outliers: If you want all zero coverage positions to be treated like outliers then use this flag. The reason to treat zero coverage as outliers is because when mapping reads to a reference we could get many zero positions due to accessory genes. These positions then skew the average values that we compute.
--outliers-threshold NUM: Threshold to use for the outlier detection. The default value is '1.5'. Absolute deviation around the median is used. To read more about the method please refer to: 'How to Detect and Handle Outliers' by Boris Iglewicz and David Hoaglin (doi:10.1016/j.jesp.2013.03.013). Default: 1.5

PARAMETERS OF CONVENIENCE They say they save lives.

--just-do-it: Don't bother me with questions or warnings, just do it.

INSEQ DATA When analyzing INSeq/Tn-Seq data

--inseq-stats: Provide if working with INSeq/Tn-Seq genomic data. With this, all gene level coverage stats will be calculated using INSeq/Tn-Seq statistical methods.

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.