cDNA / transcriptome mapping option "-cdna": To specify a cDNA / transcriptome mapping project, use the -cdna option with the runMapping or newMapping commands.

cDNA reference option “-cref”: To specify a cDNA (transcript) reference sequence for the mapping project, use the -cref option on the command line for the setRef command or with the runMapping, newMapping, or runProject commands.

cDNA reference option “-gref”: To specify a gDNA (genomic DNA) reference sequence for the mapping project, use the -gref option on the command line for the setRef command or with the runMapping, newMapping, or runProject commands.

Renaming file option “-accno”: To specify a tab-delimited file containing annotation data, use the –accno option (see more details on the use of this option in the next section).

refGene file option “-annot”: To specify a tab-delimited file containing gene, transcript, and exon information, use the ‑annot option (see more details on the use of this option are in the next section).

The reference type (cDNA or gDNA) can be automatically detected under certain circumstances, thus removing the need to specify the reference type on the command line. The logic employed depends on whether or not the GOLDENPATH environmental variable is in use. See Appendix 5.4.