Rationale and background:
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Step 1: Check our mapping file for errors¶
The QIIME mapping file contains all of the per-sample metadata, including technical information such as primers and barcodes that were used for each sample, and information about the samples, including what body site they were taken from. In this current tutorial data set we're looking at human microbiome samples from four sites on the bodies of two individuals at mutliple time points. The metadata in this case therefore includes a subject identifier, a timepoint, and a body site for each sample. You can review the map.tsv file to see an example of the data (or view the published Google Spreadsheet version, which is more nicely formatted).
In this step, we run validate_mapping_file.py to ensure that our mapping file is compatible with QIIME. First we will use a perfectly normal mapping file to do test this
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$ validate_mapping_file.py -o ~/qiime_illumina_test/vmf-map/ -m map.tsv # No errors or warnings were found in mapping file. |
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$ make_emperor.py -i ~/qiime_illumina_test/cdout/bdiv_even1114/weighted_unifrac_pc.txt -o ~/qiime_illumina_test/cdout/bdiv_even1114/weighted_unifrac_emperor_pcoa_plot -m map.tsv --custom_axes DaysSinceExperimentStart $ make_emperor.py -i ~/qiime_illumina_test/cdout/bdiv_even1114/unweighted_unifrac_pc.txt -o ~/qiime_illumina_test/cdout/bdiv_even1114/unweighted_unifrac_emperor_pcoa_plot -m map.tsv --custom_axes DaysSinceExperimentStart |
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