correct default to UMI-based (88e8e5f8) · Commits · github_fork / Universc

launch_universc.sh

+20 −8

Original line number	Diff line number	Diff line
		@@ -308,7 +308,7 @@ chemistry=""
		jobmode="local"
		ncores=""
		mem=""
		nonUMI=true
		nonUMI=false
		percelldata=false

		next=false
		@@ -807,7 +807,7 @@ elif [[ "$technology" == "nadia" ]]; then
		minlength=12
		elif [[ "$technology" == "icell8" ]]; then
		barcodelength=11
		if [[ $nonUMI ]]; then
		if [[ $nonUMI == "true" ]]; then
		umilength=0
		else
		umilength=14
		@@ -815,7 +815,7 @@ elif [[ "$technology" == "icell8" ]]; then
		minlength=11
		elif [[ "$technology" == "icell8-5-prime" ]]; then
		barcodelength=10
		if [[ $nonUMI ]]; then
		if [[ $nonUMI == "true" ]]; then
		umilength=0
		else
		umilength=8
		@@ -871,7 +871,7 @@ elif [[ "$technology" == "seqwell" ]]; then
		minlength=8
		elif [[ "$technology" == "smartseq2" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "icell8-full-length" ]] \|\| [[ "$technology" == "fluidigm-c1" ]] \|\| [[ "$technology" == "c1-cage" ]] \|\| [[ "$technology" == "quartz-seq" ]] \|\| [[ "$technology" == "ramda-seq" ]] \|\| [[ "$technology" == "c1-ramda-seq" ]]; then
		barcodelength=16
		if [[ $nonUMI ]]; then
		if [[ $nonUMI == "true" ]]; then
		umilength=0
		else
		umilength=8
		@@ -2718,7 +2718,10 @@ else
		#returns a combined R1 file with I1-R1 concatenated (I1 is cell barcode)
		mv $crIN/Concatenated_File.fastq ${convR1}

		if [[ $nonUMI ]]; then
		if [[ $nonUMI == "true" ]]; then
		if [[ $verbose ]]; then
		echo "adding mock UMI"
		fi
		# add mock UMI (count reads instead of UMI) barcodelength=6, umi_default=10
		perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default
		umilength=$umi_default
		@@ -2765,6 +2768,8 @@ else
		echo " ...processsing for ${technology}"
		if [[ $verbose ]]; then
		echo "Note: ICELL8 v2 does not contain UMIs"
		echo "chem: chemistry"
		echo "non-UMI: $nonUMI"
		fi
		for convFile in "${convFiles[@]}"; do
		read=$convFile
		@@ -2788,11 +2793,15 @@ else
		fi
		fi

		if [[ $nonUMI ]]; then
		if [[ $nonUMI == "true" ]]; then
		if [[ $chemistry == "SC3P"* ]] && [[ "$technology" == "icell8" ]]; then
		if [[ $verbose ]]; then
		echo "remove UMI to replace with mock"
		fi
		#remove inflated umi (to replace with mock and count as reads)
		sed -E '
		/^(.{11})(.{14})(.*)/ {
		/^@/ {
		n
		s/^(.{11})(.{14})(.*)/\1\3/g
		n
		n
		@@ -2801,6 +2810,9 @@ else
		mv ${crIN}/.temp $convFile
		fi

		if [[ $verbose ]]; then
		echo "adding mock UMI"
		fi
		# add mock UMI (count reads instead of UMI) barcodelength=10 or 11, umi_default=10 <- default for "icell8-5-prime" and "icell8-full-length"
		perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default
		umilength=$umi_default
		@@ -3374,7 +3386,7 @@ else

		#replace UMI with mock UMI to count reads (for technologies not already containing mock UMI)
		if [[ $technology != "icell8" ]] && [[ $technology != "ramda-seq" ]] && [[ $technology != "quartz-seq" ]] && [[ $technology != "smartseq" ]] && [[ $technology != "smartseq2" ]] && [[ $technology != "strt-seq" ]]; then
		if [[ $nonUMI ]]; then
		if [[ $nonUMI == "true" ]]; then
		echo "WARNING: removing true UMI and replacing with Mock UMI"
		echo "NOTICE: results will result read counts not UMI"
		echo "## this behaviour is not recommended unless integrating with non-UMI data ##"

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