add support for CEL-Seq2 with barcode and UMI swap (d598dd8a) · Commits · github_fork / Universc

launch_universc.sh

+17 −2

Original line number	Diff line number	Diff line
		@@ -757,8 +757,11 @@ else
		barcodefile=${SDIR}/Quartz-Seq2-384_barcode.txt
		elif [[ "$technology" == "quartz-seq2-1536" ]]; then
		barcodefile=${SDIR}/Quartz-Seq2-1536_barcode.txt
		elif [[ "$technology" == "custom"* ]] \|\| [[ "$technology" == "celseq" ]] \|\| [[ "$technology" == "scrubseq" ]]; then
		elif [[ "$technology" == "custom"* ]] \|\| [[ "$technology" == "celseq"* ]] \|\| [[ "$technology" == "scrubseq" ]]; then
		if [[ "$technology" == "celseq" ]]; then
		customname="celseq"
		minlength=8
		elif [[ "$technology" == "celseq2" ]]; then
		customname="celseq"
		minlength=6
		elif [[ "$technology" == "scrubseq" ]]; then
		@@ -890,6 +893,9 @@ if [[ "$technology" == "10x" ]]; then
		umilength=10
		umi_default=10
		elif [[ "$technology" == "celseq" ]]; then
		barcodelength=8
		umilength=4
		elif [[ "$technology" == "celseq2" ]]; then
		barcodelength=6
		umilength=6
		elif [[ "$technology" == "nadia" ]]; then
		@@ -1175,6 +1181,15 @@ else
		echo " barcodes: ${barcodeadjust}bps at its head"
		echo " UMIs: ${umiadjust}bps at its tail"

		#for CEL-Seq2 swap barcode and UMI
		if [[ "$technology" == "sciseq" ]]; then
		for convFile in "${convFiles[@]}"; do
		#swap UMI and barcode
		sed -E '2~2s/(.{6})(.{6})/\2\1/' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#remove adapter from inDrops
		if [[ "$technology" == "indrop-v1" ]] \|\| [[ "$technology" == "indrop-v2" ]];
		for convFile in "${convFiles[@]}"; do
		@@ -1185,7 +1200,7 @@ else
		done
		fi

		#remove adapter from Sci-Seq
		#remove adapter from Sci-Seq and swap barcode and UMI
		if [[ "$technology" == "sciseq" ]]; then
		for convFile in "${convFiles[@]}"; do
		#remove adapter if detected

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