generate split-seq2 barcodes and trim adapters (49bdebf9) · Commits · github_fork / Universc

launch_universc.sh

+37 −5

Original line number	Diff line number	Diff line
		@@ -1684,6 +1684,15 @@ else
		> ${whitelistdir}/sciseq3_barcode.txt
		## to filter unique lines: awk '!a[$0]++' > ${whitelistdir}/sciseq3_barcode.txt
		fi
		elif [[ "$technology" == "splitseq" ]] \|\| [[ "$technology" == "splitseq2" ]]; then
		#generates all combinations of I1-I2-R1 barcodes
		if [[ ! -f ${whitelistdir}/splitseq2_barcode.txt ]]; then
		join -j 9999 ${whitelistdir}/split-seq_round1_barcode.txt ${whitelistdir}/split-seq_round2_barcode.txt \| sed "s/ //g" \| \
		join -j 9999 - ${whitelistdir}/split-seq_round3_barcode.txt \| sed "s/ //g" \| awk '!a[$0]++' > ${whitelistdir}/splitseq2_barcode.txt
		fi
		if [[ ! -f ${whitelistdir}/splitseq_barcode.txt ]]; then
		cp ${whitelistdir}/splitseq2_barcode.txt ${whitelistdir}/splitseq_barcode.txt
		fi
		elif [[ "$technology" == "strt-seq-2i" ]]; then
		if [[ ! -f ${whitelistdir}/STRTSeq2i_barcode.txt ]]; then
		#generates all combinations of I1-I2-R1 barcodes
		@@ -2446,9 +2455,9 @@ else
		for convFile in "${convFiles[@]}"; do
		read=$convFile
		convR1=$read
		convR2=$(echo $read \| perl -pne 's/(.*)_R1/$1_R2/' )
		convI1=$(echo $read \| perl -pne 's/(.*)_R1/$1_I1/' )
		convI2=$(echo $read \| perl -pne 's/(.*)_R1/$1_I2/' )
		convR2=$(echo $read \| perl -pne 's/(.*)_R2/$1_R1/' )
		convI1=$(echo $read \| perl -pne 's/(.*)_R2/$1_I1/' )
		convI2=$(echo $read \| perl -pne 's/(.*)_R2/$1_I2/' )

		# (R1 -> R2; R2 -> I1; R3 -> I2; R4 -> R1)
		# v3 : summer 2016 redesign requiring manual demultiplexing.
		@@ -2665,10 +2674,10 @@ else
		done
		fi

		#SPLiT-Seq: correct phase blocks and swap barcode and UMI (if a whitelist and 18bp barcode can be supported)
		#SPLiT-Seq: correct phase blocks and swap barcode and UMI (if a whitelist and 24 bp barcode can be supported)
		## https://github.com/hms-dbmi/dropEst/issues/80
		## https://github.com/sdparekh/zUMIs/wiki/Protocol-specific-setup
		if [[ "$technology" == "splitseq" ]] \|\| [[ "$technology" == "splitseq2" ]]; then
		if [[ "$technology" == "splitseq" ]]; then
		echo " ...remove adapter and phase blocks for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers (swap barcode and UMI)
		@@ -2683,6 +2692,29 @@ else
		echo " ...barcode and UMI swapped for ${technology}" #performed by \1 above
		done
		fi
		if [[ "$technology" == "splitseq2" ]]; then
		echo " ...remove adapter and phase blocks for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers
		sed -E '
		/.*CGAATGCTCTGGCCTTCGGACGATCATGGG(.{8})CAAGTATGCAGCGCGCTCAAGCACGTGGAT(.{8})AGTCGTACGCCGATGCGAAACATCGGCCAC(.{8})(.{10})$/ {
		s/.*CGAATGCTCTGGCCTTCGGACGATCATGGG(.{8})CAAGTATGCAGCGCGCTCAAGCACGTGGAT(.{8})AGTCGTACGCCGATGCGAAACATCGGCCAC(.{8})(.{10})$/\1\2\3\4/g
		n
		n
		s/.*.{30}(.{8}).{30}(.{8}).{30}(.{8})(.{10})$/\1\2\3\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#remove phase blocks and linkers (reverse complement if R2 matched)
		sed -E '
		/^(.{10})(.{8})GTGGCCGATGTTTCGCATCGGCGTACGACT(.{8})ATCCACGTGCTTGAGCGCGCTGCATACTTG(.{8})CCCATGATCGTCCGAAGGCCAGAGCATTCG/ {
		s/^(.{10})(.{8})GTGGCCGATGTTTCGCATCGGCGTACGACT(.{8})ATCCACGTGCTTGAGCGCGCTGCATACTTG(.{8})CCCATGATCGTCCGAAGGCCAGAGCATTCG/\4\3\2\1/g
		n
		n
		s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})$/\4/3/2/1/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#SCRB-Seq: remove adapter
		## https://teichlab.github.io/scg_lib_structs/methods_html/SCRB-seq.html

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