update smart-seq3 default barcodes to nextera dual indexes (752d4514) · Commits · github_fork / Universc

launch_universc.sh

+5 −2

Original line number	Diff line number	Diff line
		@@ -1799,7 +1799,10 @@ else
		echo " ...generating combination of I1, I2, and RT barcodes..."
		fi
		elif [[ "$technology" == "smartseq2" ]] \|\| [[ "$technology" == "smartseq3" ]]; then
		barcodefile=${whitelistdir}/SmartSeq3_barcode.txt
		barcodefile=${whitelistdir}/Illumina_Nextera_dual_barcodes.txt
		if [[ ! -f ${whitelistdir}/Illumina_Nextera_dual_barcodes.txt ]]; then
		echo " ...generating combination of I1 and I2 barcodes..."
		fi
		elif [[ "$technology" == "strt-seq" ]]; then
		barcodefile=${whitelistdir}/STRTSeq_barcode.txt
		elif [[ "$technology" == "strt-seq-c1" ]]; then
		@@ -1852,7 +1855,7 @@ else
		join -j 9999 ${whitelistdir}/bd_rhapsody_cell_label_section1.txt ${whitelistdir}/bd_rhapsody_cell_label_section2.txt \| sed "s/ //g" \| \
		join -j 9999 - ${whitelistdir}/bd_rhapsody_cell_label_section3.txt \| sed "s/ //g" > ${whitelistdir}/bd_rhapsody_barcode.txt
		fi
		elif [[ "$technology" == "fluidigm-c1" ]] \|\| [[ "$technology" == "c1-cage" ]] \|\| [[ "$technology" == "ramda-seq" ]] \|\| [[ "$technology" == "c1-ramda-seq" ]]; then
		elif [[ "$technology" == "fluidigm-c1" ]] \|\| [[ "$technology" == "c1-cage" ]] \|\| [[ "$technology" == "ramda-seq" ]] \|\| [[ "$technology" == "c1-ramda-seq" ]] \|\| [[ "$technology" == "smartseq2" ]] \|\| [[ "$technology" == "smartseq3" ]]; then
		if [[ ! -f ${whitelistdir}/Illumina_Nextera_dual_barcodes.txt ]];then
		#generates all combinations of I1-I2 barcodes
		join -j 9999 ${whitelistdir}/Illumina_Nextera_Index1_i7_barcodes.txt ${whitelistdir}/Illumina_Nextera_Index1_i5_barcodes.txt \| sed "s/ //g" > ${whitelistdir}/Illumina_Nextera_dual_barcodes.txt

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