From 33cc39e8d014e6e1bbcd76f8d2afc27b09fedbaf Mon Sep 17 00:00:00 2001 From: nkleinbo Date: Thu, 26 Sep 2019 14:42:39 +0200 Subject: [PATCH] Update ReadMapping.rst --- docs/read_qc/ReadMapping.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/read_qc/ReadMapping.rst b/docs/read_qc/ReadMapping.rst index 4bbed25..7b99163 100644 --- a/docs/read_qc/ReadMapping.rst +++ b/docs/read_qc/ReadMapping.rst @@ -106,7 +106,7 @@ We now use graphmap to align the different read sets to the reference, starting cd ~/workdir mkdir ~/workdir/map_to_ref - graphmap align -r ~/workdir/data/Reference.fna -t 14 -C -d ~/workdir/basecall/basecall.fastq.gz -o ~/workdir/map_to_ref/nanopore.graphmap.sam > ~/workdir/map_to_ref/nanopore.graphmap.sam.log 2>&1 + graphmap align -r ~/workdir/data/Reference.fna -t 14 -c -d ~/workdir/basecall/basecall.fastq.gz -o ~/workdir/map_to_ref/nanopore.graphmap.sam > ~/workdir/map_to_ref/nanopore.graphmap.sam.log 2>&1 For the illumina reads we will use another aligner, as this one is more suited for this kind of data. But before we can do so, we need to create an index structure on the reference::