I’d like to limit my blast results by a minimum percent identity score within the Blast2RMA function (similar to what is available within the GUI interface). Would it be possible to include that parameter? Currently I think we can only limit by bitscore and evalue.
Here are the current parameters I found for the Blast2RMA function:
-lg, --longReads Parse and analyse as long reads. Default value: false.
-m, --maxMatchesPerRead [number] Max matches per read. Default value: 100.
-class, --classify Run classification algorithm. Default value: true.
-ms, --minScore [number] Min score. Default value: 50.0.
-me, --maxExpected [number] Max expected. Default value: 0.01.
-top, --topPercent [number] Top percent. Default value: 10.0.
-supp, --minSupportPercent [number] Min support as percent of assigned reads (0==off). Default value: 0.01.
-sup, --minSupport [number] Min support (0==off). Default value: 0.
-mrc, --minPercentReadCover [number] Min percent of read length to be covered by alignments. Default value: 0.0.
-alg, --lcaAlgorithm [string] Set the LCA algorithm to use for taxonomic assignment. Default value: naive. Legal values: naive, weighted, longReads
-lcp, --lcaCoveragePercent [number] Set the percent for the LCA to cover. Default value: 100.0.
-ram, --readAssignmentMode [string] Set the read assignment mode. Default value: readCount. Legal values: readCount, readLength, alignedBases, readMagnitude