warning if using Smart-Seq3 (2d210208) · Commits · github_fork / Universc

launch_universc.sh

+5 −1

Original line number	Diff line number	Diff line
		@@ -749,7 +749,7 @@ else
		echo "No barcodes whitelists available for Drop-Seq or Nadia: all possible barcodes accepted (valid barcodes will be 100% as a result)"
		echo {A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} \| sed 's/ /\n/g' \| sort \| uniq > ${barcodefile}
		fi
		elif [[ "$technology" == "icell8" ]] \|\| [[ "$technology" == "smartseq" ]]; then
		elif [[ "$technology" == "icell8" ]]; then
		barcodefile=${SDIR}/iCell8_barcode.txt
		elif [[ "$technology" == "indrop-v1" ]] \|\| [[ "$technology" == "indrop-v2" ]]; then
		barcodefile=${SDIR}/inDrops_barcodes.txt
		@@ -757,6 +757,10 @@ else
		barcodefile=${SDIR}/Quartz-Seq2-384_barcode.txt
		elif [[ "$technology" == "quartz-seq2-1536" ]]; then
		barcodefile=${SDIR}/Quartz-Seq2-1536_barcode.txt
		elif [[ "$technology" == "smartseq" ]]; then
		echo "*WARNING: barcodes not available for Smart-Seq 2 or 3, using iCELL8 whitelist (version 3)*"
		echo "...valid barcodes may be an overestimate"
		barcodefile=${SDIR}/iCell8_barcode.txt
		elif [[ "$technology" == "custom"* ]] \|\| [[ "$technology" == "celseq"* ]] \|\| [[ "$technology" == "scrubseq" ]]; then
		if [[ "$technology" == "celseq" ]]; then
		customname="celseq"