enable 5' runs with full R1 (97bbd118) · Commits · github_fork / Universc

launch_universc.sh

+8 −2

Original line number	Diff line number	Diff line
		@@ -2133,6 +2133,12 @@ else
		fi
		fi

		if [[ $chemistry == "SC5P"* ]] \|\| [[ $chemistry == "five"* ]]; then
		r=""
		else
		r="--r1-length=$totallength"
		fi

		#outputting command
		echo "running cellranger ..."
		echo ""
		@@ -2142,7 +2148,7 @@ start=`date +%s`
		echo "cellranger count --id=$id\\
		--fastqs=$crIN\\
		--lanes=$LANE\\
		--r1-length=$totallength\\
		$r\\
		--chemistry=$chemistry\\
		--transcriptome=$reference\\
		--sample=$SAMPLE\\
		@@ -2161,7 +2167,7 @@ echo "##########"
		cellranger count --id=$id \
		--fastqs=$crIN \
		--lanes=$LANE \
		--r1-length=$totallength \
		$r\\
		--chemistry=$chemistry \
		--transcriptome=$reference \
		--sample=$SAMPLE \