add support for Smart-Seq version 2-UMI (intermeidiate) and 3 (23f11fb4) · Commits · github_fork / Universc

launch_universc.sh

+11 −3

Original line number	Diff line number	Diff line
		@@ -77,8 +77,9 @@ 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
		Quartz-Seq2 (14bp barcodes, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcodes, 8bp UMI): quartzseq2-1536
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		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 "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10
		@@ -483,6 +484,10 @@ if [[ "$technology" == "scrubseq" ]] \|\| [[ "$technology" == "scrub-seq" ]]; then
		echo "Running with SCRUB-Seq parameters"
		technology="scrubseq"
		fi
		if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smart-seq" ]] \|\| [[ "$technology" == "smartseq2" ]] \|\| [[ "$technology" == "smart-seq2" ]] \|\| [[ "$technology" == "smartseq2-umi" ]] \|\| [[ "$technology" == "smart-seq2-umi" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "smart-seq3" ]]; then
		echo "Running with Smart-Seq3 parameters (version 3 with UMIs)"
		technology="smartseq"
		fi


		#check if technology matches expected inputs
		@@ -729,7 +734,7 @@ 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" ]]; then
		elif [[ "$technology" == "icell8" ]] \|\| [[ "$technology" == "smartseq" ]]; then
		barcodefile=${SDIR}/iCell8_barcode.txt
		elif [[ "$technology" == "indrop-v1" ]] \|\| [[ "$technology" == "indrop-v2" ]]; then
		barcodefile=${SDIR}/inDrops_barcodes.txt
		@@ -872,6 +877,9 @@ elif [[ "$technology" == "quartz-seq2-1536" ]]; then
		elif [[ "$technology" == "scrubseq" ]]; then
		barcodelength=6
		umilength=10
		elif [[ "$technology" == "smartseq" ]]; then
		barcodelength=11
		umilength=8
		else
		custom=`echo $technology \| grep -o "_" \| wc -l`
		custom=$(($custom+1))

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