add support for SureCell configuration (851a0751) · Commits · github_fork / Universc

launch_universc.sh

+36 −4

Original line number	Diff line number	Diff line
		@@ -73,7 +73,7 @@ Mandatory arguments to long options are mandatory for short options too.
		Supported technologies:
		10x Genomics (16bp barcode, 10bp UMI): 10x, chromium (v2 or v3 automatically detected)
		CEL-Seq (6bp barcode, 6bp UMI): celseq
		Drop-Seq (12pb barcode, 8pm UMI): nadia, dropseq
		Drop-Seq (12bp barcode, 8pm UMI): nadia, dropseq
		iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2
		@@ -83,6 +83,7 @@ Mandatory arguments to long options are mandatory for short options too.
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq
		SCRUB-Seq (6bp barcode, 10bp UMI): scrubseq
		SureCell (18bp barcode, 8bp UMI): surecell, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10
		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)
		@@ -503,9 +504,14 @@ if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smart-seq" ]] \|\| [[
		echo "*WARNING: Smart-Seq settings should only be used for kits that have UMIs*"
		technology="smartseq"
		fi
		if [[ "$technology" == "surecell" ]] \|\| [[ "$technology" == "surecellseq" ]] \|\| [[ "$technology" == "surecell-seq" ]]\|\| [[ "$technology" == "bioraad" ]]; then
		echo "Running with SureCell parameters"
		technology="surecell"
		fi


		if [[ "$technology" == "indrop-v3" ]] \
		\|\| [[ "$technology" == "indrop"* ]] \
		\|\| [[ "$technology" == "sciseq" ]] \
		\|\| [[ "$technology" == "smart-seq"* ]]; then
		## see the following issues from supporting inDrops-v3
		# https://github.com/alexdobin/STAR/issues/825
		@@ -525,7 +531,8 @@ if [[ "$technology" != "10x" ]] \
		&& [[ "$technology" != "quartz-seq2"* ]] \
		&& [[ "$technology" != "sciseq" ]] \
		&& [[ "$technology" != "scrubseq" ]] \
		&& [[ "$technology" != "smart-seq"* ]]; then
		&& [[ "$technology" != "smart-seq"* ]]\
		&& [[ "$technology" != "surecell" ]]; then
		if [[ "$technology" != "custom"* ]]; then
		echo "Error: option -t needs to be 10x, nadia, icell8, or custom_<barcode>_<UMI>"
		exit 1
		@@ -780,16 +787,23 @@ else
		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
		elif [[ "$technology" == "custom"* ]] \|\| [[ "$technology" == "celseq"* ]] \|\| [[ "$technology" == "scrubseq" ]] \|\| [[ "$technology" == "sciseq" ]] \|\| [[ "$technology" == "surecell" ]]; then
		if [[ "$technology" == "celseq" ]]; then
		customname="celseq"
		minlength=8
		elif [[ "$technology" == "celseq2" ]]; then
		customname="celseq"
		minlength=6
		elif [[ "$technology" == "sciseq" ]]; then
		customname="sciseq"
		minlength=10
		elif [[ "$technology" == "scrubseq" ]]; then
		customname="scrubseq"
		minlength=6
		elif [[ "$technology" == "surecell" ]]; then
		customname="surecell"
		barcodelength=18
		minlength=$(( $barcodelength < 16 ? $barcodelength : 16 ))
		elif [[ "$technology" == "custom"* ]]; then
		custom=`echo $technology \| grep -o "_" \| wc -l`
		custom=$(($custom+1))
		@@ -948,6 +962,9 @@ elif [[ "$technology" == "scrubseq" ]]; then
		elif [[ "$technology" == "smartseq" ]]; then
		barcodelength=11
		umilength=8
		elif [[ "$technology" == "surecell" ]]; then
		barcodelength=18
		umilength=8
		else
		custom=`echo $technology \| grep -o "_" \| wc -l`
		custom=$(($custom+1))
		@@ -1251,6 +1268,21 @@ else
		done
		fi

		#remove adapter from SureCell (and correct phase blocks)
		if [[ "$technology" == "surecell" ]];
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers
		sed -E '
		/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/ {
		s/.(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC./\1\2\3\4/g
		n
		n
		s/.*(.{6}).{15}(.{6}).{15}(.{6}).{3}(.{8}).{3}/\1\2\3\4/g
		}' $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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