run SCI-Seq test job successfully (with correct indices) (f16e5f3b) · Commits · github_fork / Universc

launch_universc.sh

+14 −16

Original line number	Diff line number	Diff line
		@@ -2447,31 +2447,29 @@ else
		for convFile in "${convFiles[@]}"; do
		#remove adapter if detected (and keep hairpin/tn5 barcode)
		## TruSeq adapter: ACGACGCTCTTCCGATCT
		sed -E '
		cat $convFile \| sed -E '
		/^ACGACGCTCTTCCGATCT/ {
		s/^ACGACGCTCTTCCGATCT//g
		n
		n
		s/^.{18}//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		}' \|
		#remove linker (10 bp barcodes)
		sed -E '
		/^(.{10})CAGAGC/ {
		s/^(.{10})CAGAGC(.{18})/\1\2/g
		/^(.{9})CAGAGC/ {
		s/^(.{9})CAGAGC(.{18})/T\1CAGAGC\2/g
		n
		n
		s/^(.{10})(.{6})(.{18})/\1\3/g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		s/^(.{9})(.{6})(.{18})/F\1\2\3/g
		}' \|
		#remove linker (9 bp barcodes)
		sed -E '
		/^(.{9})CAGAGC/ {
		s/^(.{9})CAGAGC(.{18})/E\1\2/g
		/^(.{10})CAGAGC/ {
		s/^(.{10})CAGAGC/\1/g
		n
		n
		s/^(.{9})(.{6})(.{18})/F\1\3/g
		}' $convFile > ${crIN}/.temp
		s/^(.{10})(.{6})/\1/g
		}' > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#swap barcode and UMI
		echo " ...barcode and UMI swapped for ${technology}"