Use --interleaved for bowtie2

bigdatagenomics · May 12, 2017 · 64ddceb · 64ddceb
1 parent 82ef700
commit 64ddceb
Showing 1 changed file with 1 addition and 3 deletions.
diff --git a/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala b/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala
@@ -75,9 +75,7 @@ class Bowtie2(protected val args: Bowtie2Args) extends BDGSparkCommand[Bowtie2Ar
     implicit val tFormatter = InterleavedFASTQInFormatter
     implicit val uFormatter = new AnySAMOutFormatter
 
-    // currently using -U for unpaired reads, results will suffer accordingly
-    // fix is to use --tab5/6, see https://github.com/bigdatagenomics/adam/issues/1377
-    val bowtie2Command = "bowtie2 -x " + args.indexPath + " -U -"
+    val bowtie2Command = "bowtie2 -x " + args.indexPath + " --interleaved -"
     val output: AlignmentRecordRDD = input.pipe[AlignmentRecord, AlignmentRecordRDD, InterleavedFASTQInFormatter](bowtie2Command)
       .transform(_.cache())