genes-of-interest-txt

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

Required or used by

anvi-display-structure anvi-export-functions anvi-export-gene-coverage-and-detection anvi-export-structures anvi-gen-fixation-index-matrix anvi-gen-gene-consensus-sequences anvi-gen-structure-database anvi-gen-variability-profile anvi-profile-blitz anvi-update-structure-database

Description

Some anvi’o programs that analyze genes allow the user to specify gene caller IDs to work on (i.e., instead of all genes in a contigs-db). This can sometimes be done via the command line parameter --gene-caller-ids, which accepts a list (often comma-delimited) of gene caller IDs, and sometimes via the command line parameter --genes-of-interest, which accepts a file in which the gene caller IDs are stored.

The input file for --genes-of-interest looks like the following example, with every line of the file corresponding to a single, integer gene caller ID:

5
13
79
148
206

Ideally, each gene caller ID would match to those stored in the contigs-db currently being analyzed. But if this is not the case, some anvi’o programs will throw you an error to let you know of any mismatches.

Edit this file to update this information.