Microorganism Reporting File format
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First, we recommend saving the provided template file with a new name
Do not add any new columns and do not delete any columns from the template file
Do not change or remove any text from the header row. **The "kmer_read_count" metric is only valid with the UPIP enrichment panel.
Rows with microorganism names that are not of interest can be deleted. However, the entire tiered reporting group for certain viruses must be included to preserve tiered reporting logic (if desired). Membership in a tiered reporting group means that a hierarchical relationship is pre-built into the database and the most granular tier level passing reporting thresholds is reported. For example, if Influenza B virus (B/Victoria/2/87-like) or Influenza B virus (B/Yamagata/16/88-like) are reported in a sample then the less granular Influenza B virus reporting name will NOT be reported. See the "Has Tiered Reporting" and "Reporting Tier" columns of the "Microorganisms" table in the for RPIP, RVOP/RVEK, VSP, and VSP V2 to select and see which viruses are reported as part of a tiered reporting group.
Upload the microorganism reporting file to a BaseSpace Project. **It is only necessary to upload the file once.
Select the file by clicking on the "Dataset File(s)" option under the "User-defined specification" section.
See example below for 6 RPIP microorganism reporting names. Prediction logic can be specified on a microorganism-by-microorganism basis using multiple parameters and combinatorial logical expressions.
Acinetobacter baumannii
default
Cryptococcus neoformans
coverage
0.3
Escherichia coli
aligned_read_count
200
Human adenovirus E
(coverage AND median_depth) OR (aligned_read_count AND ani)
0.1
1
0.95
100
Human bocavirus 1 (HBoV1)
rpkm OR (ani AND coverage) OR median_depth
0.2
5
0.9
5
Klebsiella pneumoniae
default AND coverage
0.5