diff --git a/RiboCode/prepare_transcripts.py b/RiboCode/prepare_transcripts.py
index f44b5fe..4a54631 100644
--- a/RiboCode/prepare_transcripts.py
+++ b/RiboCode/prepare_transcripts.py
@@ -369,6 +369,9 @@ def processTranscripts(genomeFasta,gtfFile,out_dir):
 		transcript_seq_file.close()
 		transcript_cds_file.close()
 
+		sys.stderr.write("\tBuilding the transcripts_sequence.fa pyfasta index\n")
+		GenomeSeq(os.path.join(out_dir,"transcripts_sequence.fa"))
+
 		## dump the pickle
 		sys.stderr.write("\tSaving the transcripts.pickle\n")
 		with open(pickle_file,"wb") as fout: