diff --git a/bcbio/rnaseq/cufflinks.py b/bcbio/rnaseq/cufflinks.py
index <HASH>..<HASH> 100644
--- a/bcbio/rnaseq/cufflinks.py
+++ b/bcbio/rnaseq/cufflinks.py
@@ -93,7 +93,7 @@ def _get_output_dir(align_file, data, sample_dir=True):
 def assemble(bam_file, ref_file, num_cores, out_dir, data):
     out_dir = os.path.join(out_dir, data["rgnames"]["sample"])
     safe_makedir(out_dir)
-    out_file = os.path.join(out_dir, data["rgnames"]["sample"], "transcripts.gtf")
+    out_file = os.path.join(out_dir, "transcripts.gtf")
     if file_exists(out_file):
         return out_file
     with file_transaction(data, out_dir) as tmp_out_dir:
Return proper output for transcriptome assembly.

This was broken by this fix: <I>b<I>b<I>b<I>b8.