diff --git a/bio/star/align/meta.yaml b/bio/star/align/meta.yaml
index 4d00c29a7b..0ebb5f6c99 100644
--- a/bio/star/align/meta.yaml
+++ b/bio/star/align/meta.yaml
@@ -5,6 +5,7 @@ authors:
   - Johannes Köster
   - Tomás Di Domenico
   - Filipe G. Vieira
+  - Kashyap Chhatbar
 notes: |
   * The `extra` param allows for additional program arguments.
   * It is advisable to consider updating the limits setting before running STAR,
diff --git a/bio/star/align/test/Snakefile b/bio/star/align/test/Snakefile
index 460119108c..5c05466db0 100644
--- a/bio/star/align/test/Snakefile
+++ b/bio/star/align/test/Snakefile
@@ -12,6 +12,7 @@ rule star_pe_multi:
         aln="star/pe/{sample}/pe_aligned.sam",
         log="logs/pe/{sample}/Log.out",
         sj="star/pe/{sample}/SJ.out.tab",
+        unmapped=["star/pe/{sample}/unmapped.1.fastq.gz","star/pe/{sample}/unmapped.2.fastq.gz"],
     log:
         "logs/pe/{sample}.log",
     params:
@@ -32,6 +33,7 @@ rule star_se:
         aln="star/se/{sample}/se_aligned.bam",
         log="logs/se/{sample}/Log.out",
         log_final="logs/se/{sample}/Log.final.out",
+        unmapped="star/se/{sample}/unmapped.fastq",
     log:
         "logs/se/{sample}.log",
     params:
diff --git a/bio/star/align/wrapper.py b/bio/star/align/wrapper.py
index 2b240b1a34..85033d1768 100644
--- a/bio/star/align/wrapper.py
+++ b/bio/star/align/wrapper.py
@@ -42,6 +42,9 @@
 else:
     readcmd = ""
 
+out_unmapped = snakemake.output.get("unmapped", "")
+if out_unmapped:
+    out_unmapped = "--outReadsUnmapped Fastx"
 
 index = snakemake.input.get("idx")
 if not index:
@@ -64,6 +67,7 @@
         " --readFilesIn {input_str}"
         " {readcmd}"
         " {extra}"
+        " {out_unmapped}"
         " --outTmpDir {tmpdir}/STARtmp"
         " --outFileNamePrefix {tmpdir}/"
         " --outStd {stdout}"
@@ -83,3 +87,12 @@
         shell("cat {tmpdir}/Log.progress.out > {snakemake.output.log_progress:q}")
     if snakemake.output.get("log_final"):
         shell("cat {tmpdir}/Log.final.out > {snakemake.output.log_final:q}")
+    unmapped = snakemake.output.get("unmapped")
+    if unmapped:
+        # SE
+        if not fq2:
+            unmapped = [unmapped]
+
+        for i, out_unmapped in enumerate(unmapped, 1):
+            cmd = "gzip -c" if out_unmapped.endswith("gz") else "cat"
+            shell("{cmd} {tmpdir}/Unmapped.out.mate{i} > {out_unmapped}")