Overview of the files in the genomes/counts folder.

[LeeBergstrand]

I am trying to determine each dereplicated MAG's abundance in each sample.

The counts folder within genomes contains four files:

• counts_genomes.parquet
• binned_coverage.parquet
• coverage_contigs.parquet
• median_coverage_genomes.parquet

Can you provide an overview of what each file contains and how each is generated?

For example, the counts_genomes.parquet file appears to contain the number of reads mapping from each metagenome to each MAG. Is this correct?

[SilasK]

So we map the reads to the combined set of contigs of the representative MAGs.

• counts_genomes.parquet contains the raw counts per genome
• coverage_contigs.parquet contains the coverage for all contigs of the representative MAGs
• binned_coverage.parquet contains the coverage binned in 1kb? bins of the contigs
• median_coverage_genomes.parquet is the median coverage per genome based on the binned coverage.

I suggest to use the median coverage for relative abundance calculation. And the counts if you want /need counts.

[github-actions[bot]]

There was no activity since some time. I hope your issue is solved in the mean time. This issue will automatically close soon if no further activity occurs.

Thank you for your contributions.