gene-clusters-txt
Table of Contents
A TXT-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use.
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Description
A three-column TAB-delimited file with a specific header line to link genes across genomes to one another through ‘gene clusters’.
The primary purpose of this file is to provide a means for the user to let the anvi’o know about their gene clusters, rather than computing gene clusters through the conventional pangenomics approach implemented in anvi’o and accessible via anvi-pan-genome.
For instance, through this file the user can ask anvi-pan-genome to make use of the gene clusters they have identified in their genomes using another program, and still use downstream anvi’o programs, such as anvi-display-pan or anvi-compute-functional-enrichment-in-pan to work with the resulting pan-db.
File format
A proper gene-clusters-txt file must contain the following headers,
| genome_name | gene_caller_id | gene_cluster_name |
|---|---|---|
| (…) | (…) | (…) |
| NATL1A | 1653 | Cluster_00001777 |
| NATL1A | 1487 | Cluster_00001779 |
| NATL1A | 1294 | Cluster_00001782 |
| MIT9401 | 1571 | Cluster_00001786 |
| MIT9322 | 1069 | Cluster_00001786 |
| NATL1A | 47 | Cluster_00001794 |
| NATL1A | 714 | Cluster_00001837 |
| NATL1A | 1089 | Cluster_00001845 |
| NATL1A | 1275 | Cluster_00001849 |
| NATL1A | 644 | Cluster_00001850 |
| NATL1A | 1413 | Cluster_00001857 |
| NATL1A | 1195 | Cluster_00001868 |
| MIT9401 | 1558 | Cluster_00001872 |
| NATL1A | 1111 | Cluster_00001886 |
| NATL1A | 1074 | Cluster_00001892 |
| NATL1A | 1191 | Cluster_00001894 |
| NATL1A | 1803 | Cluster_00001898 |
| NATL1A | 1964 | Cluster_00001902 |
| NATL1A | 1332 | Cluster_00001910 |
| NATL1A | 908 | Cluster_00001912 |
| NATL1A | 1088 | Cluster_00001914 |
| NATL1A | 1497 | Cluster_00001916 |
| NATL1A | 812 | Cluster_00001923 |
| NATL1A | 1107 | Cluster_00001924 |
| NATL1A | 1165 | Cluster_00001928 |
| NATL1A | 1220 | Cluster_00001931 |
| NATL1A | 1138 | Cluster_00001942 |
| NATL1A | 706 | Cluster_00001952 |
| NATL1A | 1660 | Cluster_00001957 |
| (…) | (…) | (…) |
where,
- genome_name represents a genome name that matches to a genome that is in the genomes-storage-db,
- gene_caller_id represents a gene call in that genome,
- gene_cluster_name represents the gene cluster to which the gene is assigned.
Please note that It is possible to obtain this file for an already computed anvi’o pan-db using the program anvi-export-gene-clusters.
Edit this file to update this information.