refactor removal of adapters for clarity (d7393294) · Commits · github_fork / Universc

launch_universc.sh

+30 −16

Original line number	Diff line number	Diff line
		@@ -1035,7 +1035,7 @@ for i in ${keys[@]}; do
		done

		#inverting R1 and R2 for specific technologies
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]]; then
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]] \|\| [[ "$technology" == "splitseq" ]]; then
		#invert read1 and read2
		echo "*WARNING: technology is set to ${technology}. barcodes on Read 2 will be used*"
		tmp=$read1
		@@ -1672,9 +1672,11 @@ else
		echo " barcodes: ${barcodeadjust}bps at its head"
		echo " UMIs: ${umiadjust}bps at its tail"

		#for CEL-Seq2 swap barcode and UMI
		echo " making technology-specific modifications ..."
		#CEL-Seq2: swap barcode and UMI
		## https://github.com/BUStools/bustools/issues/4
		if [[ "$technology" == "sciseq" ]]; then
		if [[ "$technology" == "celseq2" ]]; then
		echo " ...barcode and UMI swapped for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#swap UMI and barcode
		sed -E '2~2s/(.{6})(.{6})/\2\1/' $convFile > ${crIN}/.temp
		@@ -1682,10 +1684,13 @@ else
		done
		fi

		#remove adapter from inDrops see here for details:
		#inDrops: remove adapter (see links below for details)
		## https://github.com/BUStools/bustools/issues/4
		## https://teichlab.github.io/scg_lib_structs/methods_html/inDrop.html
		## https://github.com/sdparekh/zUMIs/wiki/Protocol-specific-setup
		#note that adapters do not have to be removed for the dual-indexed inDrops-v3
		if [[ "$technology" == "indrop-v1" ]] \|\| [[ "$technology" == "indrop-v2" ]]; then
		echo " ...remove adapter for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove adapter if present
		sed -E '
		@@ -1696,14 +1701,16 @@ else
		s/^(.{8}).{22}(.{8})/\1\2/g
		}' $convFile \|
		#remove linker between barcode and UMI
		echo" ...barcode and UMI linker removed for ${technology}"
		sed -E '2~2s/^(.{8})(.{8}).{4}(.{6})/\1\2\3/g' > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#remove adapter from QuartzSeq
		#QuartzSeq: remove adapter
		if [[ "$technology" == "quartz-seq2-384" ]]; then
		for convFile in "${convFiles[@]}"; do
		echo " ...remove adapter for ${technology}"
		#remove adapter if detected
		sed -E '
		/^TATAGAATTCGCGGCCGCTCGCGATAC(.{14})(.{8})/ {
		@@ -1716,6 +1723,7 @@ else
		done
		fi
		if [[ "$technology" == "quartz-seq2-1536" ]]; then
		echo " ...remove adapter for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove adapter if detected
		sed -E '
		@@ -1729,9 +1737,9 @@ else
		done
		fi


		#remove adapter from Sci-Seq and swap barcode and UMI
		#Sci-Seq: remove adapter and swap barcode and UMI
		if [[ "$technology" == "sciseq" ]]; then
		echo " ...remove adapter for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove adapter if detected
		sed -E '
		@@ -1742,15 +1750,17 @@ else
		s/^(.{18})//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#swap UMI and barcode
		#swap barcode and UMI
		echo " ...barcode and UMI swapped for ${technology}"
		sed -E '2~2s/(.{8})(.{10})/\2\1/' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#remove adapter from SureCell (and correct phase blocks)
		#SureCell: remove adapter and correct phase blocks
		## https://github.com/Hoohm/dropSeqPipe/issues/42
		if [[ "$technology" == "surecell" ]]; then
		echo " ...remove adapter and phase blocks for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers
		sed -E '
		@@ -1764,12 +1774,13 @@ else
		done
		fi

		# SPLiT-Seq can be set up similarly if a whitelist and 18bp barcode can be supported
		#SPLiT-Seq: correct phase blocks and swap barcode and UMI (if a whitelist and 18bp barcode can be supported)
		## https://github.com/hms-dbmi/dropEst/issues/80
		## https://github.com/sdparekh/zUMIs/wiki/Protocol-specific-setup
		if [[ "$technology" == "splitseq" ]]; then
		echo " ...remove adapter and phase blocks for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers (swap UMI and barcode)
		#remove phase blocks and linkers (swap barcode and UMI)
		sed -E '
		/^([ATCGA]{92})/ {
		s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g
		@@ -1778,12 +1789,15 @@ else
		s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		echo " ...barcode and UMI swapped for ${technology}" #performed by \1 above
		done
		fi

		#remove adapter from SCRB-Seq

		#SCRB-Seq: remove adapter
		## https://teichlab.github.io/scg_lib_structs/methods_html/SCRB-seq.html
		if [[ "$technology" == "scrbseq" ]]; then
		echo " ...remove adapter for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove adapters
		sed -E '

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