adapt five prime chemistry for Smart-Seq3 (307df2be) · Commits · github_fork / Universc

launch_universc.sh

+14 −2

Original line number	Diff line number	Diff line
		@@ -792,6 +792,9 @@ temp_chemistry="SC3Pv2"
		if [[ $umilength -gt 10 ]]; then
		temp_chemistry="SC3Pv3"
		fi
		if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]];then
		temp_chemistry="SC5P-PE"
		fi
		if [[ "$technology" == "10x" ]]; then
		temp_chemistry="auto"
		fi
		@@ -1607,11 +1610,20 @@ if [[ "$technology" != "10x" ]]; then
		echo "Using 10x version 2 chemistry to support UMIs"
		chemistry="SC3Pv2"
		fi
		if [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE , or SC5P-R2"
		if [[ "$chemistry" != "threeprime" ]] && [[ "$chemistry" != "fiveprime" ]] && [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE, SC5P-R1, or SC5P-R2"
		exit 1
		fi
		fi
		if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]]; then
		if [[ "$chemistry" == "fiveprime" ]]; then
		chemistry="SC5P-PE"
		fi
		if [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		echo "Error: option --chemistry must be SC5P-PE, SC5P-R1 or SC5P-R2"
		exit
		fi
		fi
		##########