diff --git a/src/guides/bioinformatics/filtering-and-subsampling.rst b/src/guides/bioinformatics/filtering-and-subsampling.rst index e9dc77f..e69db72 100644 --- a/src/guides/bioinformatics/filtering-and-subsampling.rst +++ b/src/guides/bioinformatics/filtering-and-subsampling.rst @@ -350,7 +350,7 @@ This approach has some caveats: {n_{\text{other sequences}}} * \frac{1}{{n_{\text{other states}}}} = 100 * \frac{1}{49} - \approx 1.02 + \approx 2.04 2. Achieving a full *100 sequences from the rest of the United States* requires at least 2 sequences from each of the remaining states. This may not be @@ -366,8 +366,8 @@ An alternative approach is to decompose this into multiple schemes, each handled by a single call to ``augur filter``. Additionally, there is an extra step to combine the intermediate samples. - 1. Sample 100 sequences from Washington state. - 2. Sample 50 sequences from the rest of the United States. + 1. Sample 200 sequences from Washington state. + 2. Sample 100 sequences from the rest of the United States. 3. Combine the samples. Calling ``augur filter`` multiple times @@ -378,20 +378,20 @@ well for ad-hoc analyses. .. code-block:: bash - # 1. Sample 100 sequences from Washington state + # 1. Sample 200 sequences from Washington state augur filter \ --sequences sequences.fasta \ --metadata metadata.tsv \ --query "state == 'WA'" \ - --subsample-max-sequences 100 \ + --subsample-max-sequences 200 \ --output-strains sample_strains_state.txt - # 2. Sample 50 sequences from the rest of the United States + # 2. Sample 100 sequences from the rest of the United States augur filter \ --sequences sequences.fasta \ --metadata metadata.tsv \ --query "state != 'WA' & country == 'USA'" \ - --subsample-max-sequences 50 \ + --subsample-max-sequences 100 \ --output-strains sample_strains_country.txt # 3. Combine using augur filter @@ -428,8 +428,8 @@ system can be used. The following examples use `Snakemake`_. .. code-block:: yaml subsampling: - state: --query "state == 'WA'" --subsample-max-sequences 100 - country: --query "state != 'WA' & country == 'USA'" --subsample-max-sequences 50 + state: --query "state == 'WA'" --subsample-max-sequences 200 + country: --query "state != 'WA' & country == 'USA'" --subsample-max-sequences 100 2. Add two rules in a `Snakefile`_. If you are building a standard Nextstrain workflow, the output files should be used as input to sequence alignment. See @@ -438,8 +438,8 @@ system can be used. The following examples use `Snakemake`_. .. code-block:: python - # 1. Sample 100 sequences from Washington state - # 2. Sample 50 sequences from the rest of the United States + # 1. Sample 200 sequences from Washington state + # 2. Sample 100 sequences from the rest of the United States rule intermediate_sample: input: metadata = "data/metadata.tsv",