+## <a name="gen_trinity"></a> Generate Transcript-to-Gene-Map from Trinity Output
+
+For Trinity users, RSEM provides a perl script to generate transcript-to-gene-map file from the fasta file produced by Trinity.
+
+### Usage:
+
+ extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file
+
+trinity_fasta_file: the fasta file produced by trinity, which contains all transcripts assembled.
+map_file: transcript-to-gene-map file's name.
+