Update ReadMapping.rst

metagenomics · Sep 26, 2019 · 46e162d · 46e162d
1 parent a08bbf1
commit 46e162d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/docs/read_qc/ReadMapping.rst b/docs/read_qc/ReadMapping.rst
@@ -139,8 +139,8 @@ First, we convert the SAM files into BAM format and sort them::
 
 Then we can run **qualimap** on those BAM files now::
   
-  qualimap bamqc -bam ~/workdir/map_to_ref/nanopore.graphmap.sorted.bam -nw 5000 -nt 14 -outdir ~/workdir/map_to_ref/nanopore.graphmap
-  qualimap bamqc -bam ~/workdir/map_to_ref/illumina.bwa.sorted.bam -nw 5000 -nt 14 -outdir ~/workdir/map_to_ref/illumina.graphmap
+  qualimap bamqc -bam ~/workdir/map_to_ref/nanopore.graphmap.sorted.bam -nw 5000 -nt 14 -c -outdir ~/workdir/map_to_ref/nanopore.graphmap
+  qualimap bamqc -bam ~/workdir/map_to_ref/illumina.bwa.sorted.bam -nw 5000 -nt 14 -c -outdir ~/workdir/map_to_ref/illumina.graphmap
 
 Qualimap can also be run interactively.