In cases where Golden Path annotation data is unavailable, annotations may be obtained from the description lines for each reference sequence in reference file. The tag/value pair “gene=geneName” must be present on the description line. If “gene=geneName” is not present, transcript and/or gene descriptions can only be incorporated into the output by using a renaming file (see below).

A renaming file can be used to either provide more meaningful names for genes and/or transcripts and/or to incorporate transcript and gene descriptions into the output files. The structure of a renaming file is as follows: OLD_ID<TAB>NEW_ID<TAB>DESCRIPTION, where OLD_ID is either the transcript identifier or gene name that currently exists in the project or incoming annotation data, and NEW_ID is the new identifier you want to map to the old identifier. DESCRIPTION is the transcript- or gene-level description you want to map to the NEW_ID. Note that it is not necessary to rename a gene or transcript if all you want to do is incorporate gene- or transcript-level descriptions into the output. In this scenario, the OLD_ID and NEW_ID would be identical and would correspond to the appropriate description. Note also that it is possible to specify both transcript- and gene-level descriptions in the same renaming file. The way to do this is to put the transcript-level descriptions on the same lines as the corresponding transcript identifiers and the gene-level descriptions on the same lines as the corresponding gene identifiers.