add support for inDrops version 3 configuration (d0f3c53d) · Commits · github_fork / Universc

launch_universc.sh

+14 −3

Original line number	Diff line number	Diff line
		@@ -77,6 +77,7 @@ Mandatory arguments to long options are mandatory for short options too.
		iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1
		inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2
		inDrops version 3 (8bp barcodes, 6bp UMI): indrops-v3
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		@@ -467,7 +468,14 @@ fi
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrops-v2" ]] \|\| [[ "$technology" == "indropv2" ]] \|\| [[ "$technology" == "indropsv2" ]]; then
		echo "Running with inDrop parameters (version 2 with reads inverted)"
		technology="indrop-v2"
		fi
		if [[ "$technology" == "indrop-v3" ]] \|\| [[ "$technology" == "indrops-v3" ]] \|\| [[ "$technology" == "indropv3" ]] \|\| [[ "$technology" == "indropsv3" ]]; then
		echo "Running with inDrop parameters (version 3 with reads inverted)"
		technology="indrop-v3"
		fi
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]]; then
		#invert read1 and read2
		echo "Using barcodes on Read 2"
		tmp=$read1
		read1=$read2
		read2=$tmp
		@@ -921,7 +929,10 @@ elif [[ "$technology" == "icell8" ]]; then
		umilength=14
		elif [[ "$technology" == "indrop-v1" ]] \|\| [[ "$technology" == "indrop-v2" ]]; then
		barcodelength=19
		umilength=8
		umilength=6
		elif [[ "$technology" == "indrop-v3" ]]; then
		barcodelength=8
		umilength=6
		elif [[ "$technology" == "quartz-seq2-384" ]]; then
		barcodelength=14
		umilength=8

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