+=item B<--allele-to-gene-map> <file>
+
+Use information from <file> to provide gene_id and transcript_id information for each allele-specific transcript.
+Each line of <file> should be of the form:
+
+gene_id transcript_id allele_id
+
+with the fields separated by a tab character.
+
+This option is designed for quantifying allele-specific expression. It is only valid if '--gtf' option is not specified. allele_id should be the sequence names presented in the Multi-FASTA-formatted files.
+
+(Default: off)
+