minor update (8c0d1700) · Commits · github_fork / Universc

launch_universc.sh

+29 −12

Original line number	Diff line number	Diff line
		@@ -20,7 +20,7 @@
		install=false

		######UniverSC version#####
		universcversion="1.1.4"
		universcversion="1.1.6"
		##########


		@@ -207,9 +207,9 @@ Mandatory arguments to long options are mandatory for short options too.
		C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq
		CEL-Seq (8 bp barcode, 4 bp UMI): celseq
		CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
		Drop-Seq (12 bp barcode, 8 bp UMI): dropseq
		Drop-Seq (12 bp barcode, 8 bp UMI): dropseq, nadia
		ICELL8 3′ scRNA version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
		ICELL8 3′ scRNA version 3 (11 bp barcode, 14 bp UMI): icell8 or custom
		ICELL8 3′ scRNA version 3 (11 bp barcode, 14 bp UMI): icell8
		ICELL8 5′ scRNA with TCR OR kit (10bp barcode, NO bp UMI): icell8-5-prime
		ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length
		inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
		@@ -225,7 +225,7 @@ Mandatory arguments to long options are mandatory for short options too.
		RamDA-Seq (16 bp barcode, no UMI): ramda-seq
		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
		SCIFI-Seq (27 bp barcode, 8 bp UMI
		SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq
		SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq
		SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
		Smart-seq (16 bp barcode, No UMI): smartseq
		@@ -257,8 +257,7 @@ Mandatory arguments to long options are mandatory for short options too.
		-p, --per-cell-data Generates a file with basic run statistics along with per-cell data

		--non-umi or --read-only Force counting reads by adding or replacing UMI with a mock sequence.
		Available for: ICELL8, Smart-Seq2
		Default for: Quartz-Seq, RamDA-Seq, Smart-Seq, Smart-Seq2, STRT-Seq
		Default for: Quartz-Seq, RamDA-Seq, Smart-Seq, Smart-Seq2, STRT-Seq, ICELL8 3-prime version2

		--setup Set up whitelists for compatibility with new technology and exit
		--as-is Skips the FASTQ file conversion if the file already exists
		@@ -1172,8 +1171,9 @@ if [[ $verbose ]]; then
		fi
		for key in ${keys[@]}; do
		if [[ $verbose ]]; then
		readkey=$key
		echo "key: $key"
		fi
		readkey=$key
		list=()
		if [[ $readkey == "R1" ]]; then
		list=("${read1[@]}")
		@@ -2037,12 +2037,25 @@ if [[ "$technology" != "10x" ]]; then
		#use SC3Pv2 (umi length 10)
		echo "Using 10x version 2 chemistry to support UMIs"
		chemistry="SC3Pv2"
		umi_default=10
		fi
		if [[ "$chemistry" != "threeprime" ]] && [[ "$chemistry" != "fiveprime" ]] && [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
		echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE, SC5P-R1, or SC5P-R2"
		exit 1
		fi
		fi
		if [[ "$technology" == "10x" ]]; then
		#use SC3Pv3 (umi length 12)
		if [[ "$chemistry" != "auto" ]];then
		#use automatic chemistry detection
		echo "Detecting 10x chemistry automatically"
		chemistry="auto"
		#do not convert UMI
		umi_default=12
		umilength=${umi_default}
		umiadjust=0
		fi
		fi
		if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "icell8-5-prime" ]]; then
		if [[ $verbose ]]; then
		echo " Using $chemistry for $technology"
		@@ -2055,7 +2068,6 @@ if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[
		exit 1
		fi
		fi
		chemistry="SC3Pv2" #####KAI REMEMBER TO REMOVE THIS#####
		##########


		@@ -2460,13 +2472,18 @@ if [[ $lock -eq 0 ]]; then
		fi
		#for version 3
		cat ${v2} > ${v3}
		fi
		if [[ -f ${v3} ]]; then
		gzip -f ${v3}
		fi
		if [[ -f translation/${v3} ]]; then
		gzip -f translation/${v3}
		fi
		if [[ -f translation/${v3}.gz ]]; then
		rm translation/${v3}.gz
		awk -F , -v OFS="\t" '{print $1, "\t", $1}' $v3 > translation/${v3}
		zcat ${v3}.gz \| awk -F , -v OFS="\t" '{print $1, "\t\t\t", $1}' > translation/${v3}
		gzip -f translation/${v3}
		fi
		gzip -f ${v3}
		echo " whitelist converted"

		echo "verbose $verbose"
		@@ -3498,7 +3515,7 @@ if [[ $verbose ]]; then
		echo $chemistry
		fi

		if [[ $chemistry == "SC5P"* ]] \|\| [[ $chemistry == "five"* ]]; then
		if [[ $chemistry == "SC5P"* ]] \|\| [[ $chemistry == "five"* ]] \|\| [[ $chemistry == "auto" ]]; then
		r=""
		else
		r="--r1-length=$totallength"

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