add support for Sci-Seq (single-cell combinatorial indexing) (9cd1c0cb) · Commits · github_fork / Universc

launch_universc.sh

+27 −0

Original line number	Diff line number	Diff line
		@@ -79,6 +79,7 @@ Mandatory arguments to long options are mandatory for short options too.
		inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq
		SCRUB-Seq (6bp barcode, 10bp UMI): scrubseq
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		@@ -481,6 +482,10 @@ if [[ "$technology" == "quartz-seq2-1536" ]] \|\| [[ "$technology" == "quartzseq2-
		echo "Running with Quartz-Seq2 v3.2 parameters 1536 wells (15bp barcode)"
		technology="quartz-seq2-1536"
		fi
		if [[ "$technology" == "sciseq" ]] \|\| [[ "$technology" == "sci-seq" ]]; then
		echo "Running with Sci-Seq parameters (single-cell combinatorial indexing RNA sequencing)"
		technology="sciseq"
		fi
		if [[ "$technology" == "scrubseq" ]] \|\| [[ "$technology" == "scrub-seq" ]]; then
		echo "Running with SCRUB-Seq parameters"
		technology="scrubseq"
		@@ -499,6 +504,7 @@ if [[ "$technology" != "10x" ]] \
		&& [[ "$technology" != "icell8" ]] \
		&& [[ "$technology" != "indrop"* ]] \
		&& [[ "$technology" != "quartz-seq2"* ]] \
		&& [[ "$technology" != "sciseq" ]] \
		&& [[ "$technology" != "scrubseq" ]] \
		&& [[ "$technology" != "smart-seq"* ]]; then
		if [[ "$technology" != "custom"* ]]; then
		@@ -901,6 +907,9 @@ elif [[ "$technology" == "quartz-seq2-384" ]]; then
		elif [[ "$technology" == "quartz-seq2-1536" ]]; then
		barcodelength=15
		umilength=8
		elif [[ "$technology" == "sciseq" ]]; then
		barcodelength=10
		umilength=8
		elif [[ "$technology" == "scrubseq" ]]; then
		barcodelength=6
		umilength=10
		@@ -1176,6 +1185,24 @@ else
		done
		fi

		#remove adapter from Sci-Seq
		if [[ "$technology" == "sciseq" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove adapter if detected
		sed -E '
		/^ACGACGCTCTTCCGATCT/ {
		s/^(.{18})//g
		n
		n
		s/^(.{18})//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#swap UMI and barcode
		sed -E '2~2s/(.{8})(.{10})/\2\1/' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#converting barcodes
		echo " adjusting barcodes of R1 files"
		if [[ $barcodeadjust != 0 ]]; then

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