keeping unmapped reads

biocorecrg · Jun 21, 2019 · 9a9d2d6 · 9a9d2d6
1 parent f28c895
commit 9a9d2d6
Showing 1 changed file with 0 additions and 1 deletion.
diff --git a/lib/NGSaligner.groovy b/lib/NGSaligner.groovy
@@ -143,7 +143,6 @@
             STAR --genomeDir ${this.index} \
                  --readFilesIn ${this.reads} \
                   \$gzipped \
-                  --outSAMunmapped None \
                   --outSAMtype BAM SortedByCoordinate \
                   --runThreadN ${this.cpus} \
                   --quantMode GeneCounts \