generate microwell-seq barcodes and trim adapters (3ae9d1ce) · Commits · github_fork / Universc

launch_universc.sh

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Original line number	Diff line number	Diff line
		@@ -1660,6 +1660,12 @@ else
		#allow for barcodes in index (I1) and R1
		perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir}
		fi
		elif [[ "$technology" == "microwellseq" ]]; then
		if [[ ! -f ${whitelistdir}/microwellseq_barcode.txt ]]; then
		#generates all combinations of R1 barcodes
		join -j 9999 ${whitelistdir}/microwell-seq_barcodeA.txt ${whitelistdir}/microwell-seq_barcodeB.txt \| sed "s/ //g" \| \
		join -j 9999 - ${whitelistdir}/microwell-seq_barcodeC.txt > ${whitelistdir}/microwellseq_barcode.txt
		fi
		elif [[ "$technology" == "sciseq2" ]]; then
		#generates all combinations of I1-I2-R1 barcodes
		if [[ ! -f ${whitelistdir}/sciseq2_barcode.txt ]]; then
		@@ -2464,6 +2470,22 @@ else
		done
		fi

		#Microwell-Seq: remove linkers
		if [[ "$technology" == "microwellseq" ]]; then
		echo " ...remove adapter and phase blocks for ${technology}"
		for convFile in "${convFiles[@]}"; do
		#remove phase blocks and linkers
		sed -E '
		/.*(.{6})CGACTCACTACAGGG(.{6})TCGGTGACACGATCG(.{6})(.{6})/ {
		s/.*(.{6})CGACTCACTACAGGG(.{6})TCGGTGACACGATCG(.{6})(.{6})/\1\2\3\4/g
		n
		n
		s/.*(.{6}).{15}(.{6}).{15}(.{6})(.{6})$/\1\2\3\4/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		done
		fi

		#QuartzSeq: remove adapter
		if [[ "$technology" == "quartz-seq2-384" ]]; then
		for convFile in "${convFiles[@]}"; do

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