anvi-get-split-coverages
Table of Contents
Export splits and the coverage table from database.
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Authors
Can consume
profile-db 
contigs-db collection 
bin 
Can provide
Usage
This program returns the nucleotide-level coverage data for a specific set of the splits or gene in your profile-db.
If you want to get the coverage data for all splits in your profile-db, run anvi-export-splits-and-coverages with the flag --splits-mode.
Simply provide a profile-db and contigs-db pair and specify which splits, or gene, you want to look at. You have three ways to do this:
- Provide a single split name. (You can list all splits available with
--list-splits)
anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ --split-name Day17a_QCcontig9_split_00003
- Provide both the name of a bin and the collection it is contained in.
anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ -b bin \ -C collection
You can list all collections available with --list-collections or all bins in a collection with --list-bins. Alternatively, you could run anvi-show-collections-and-bins on your profile-db to get a more comprehensive overview.
- Provide a gene caller id and a flanking size (bp).
anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ --gene-caller-id 25961 \ --flank-length 500
Edit this file to update this information.
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.