Merge branch 'dev' of github.com:minoda-lab/universc into dev (393cbaa1) · Commits · github_fork / Universc

launch_universc.sh

+1 −25

Original line number	Diff line number	Diff line
		@@ -3343,7 +3343,7 @@ else
		echo " ...remove internal for ${technology} by matching tag sequence for UMI reads"
		# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as adapters
		perl ${FILTERSMARTSEQREADUMI} --r1 ${convR1} --r2 ${convR2} --i1 ${convI1} --i2 ${convI2} --tag 'ATTGCGCAATG' --out_dir ${crIN}
		echo " ...trim tag sequence from R1"
		echo " ...parsing reads with tag sequence and swoping 10x TSO for R1"

		# returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2
		mv $crIN/parsed_R1.fastq ${convR1}
		@@ -3367,30 +3367,6 @@ else
		cp ${convR1} $crIN/Concatenated_File.fastq
		fi

		#convert TSO to expected length for 10x 5' (TSS in R1 from base 39)
		echo " handling $convFile ..."
		tsoS="TTTCTTATATGGG"
		tsoQ="IIIIIIIIIIIII"
		#Add 10x TSO characters to the end of the sequence
		cmd=$(echo 'sed -E "2~4s/^(.{'$barcodelength'})(.{'${umilength}'})(.{'3'})/\1\2'$tsoS'/" '$convFile' > '${crIN}'/.temp')
		if [[ $verbose ]]; then
		echo technology $technology
		echo barcode: $barcodelength
		echo umi: $umilength
		echo $cmd
		fi
		# run command with barcode and umi length, e.g.,: sed -E "2~4s/^(.{16})(.{8})(.{'3'})(.*)/\1\2$tsoS\4/" $convFile > ${crIN}/.temp
		eval $cmd
		mv ${crIN}/.temp $convFile
		#Add n characters to the end of the quality
		cmd=$(echo 'sed -E "4~4s/^(.{'$barcodelength'})(.{'${umilength}'})(.{'3'})/\1\2'$tsoQ'/" '$convFile' > '${crIN}'/.temp')
		# run command with barcode and umi length, e.g.,: sed -E "4~4s/^(.{16})(.{8})(.{'3'})(.*)/\1\2$tsoQ\4/" $convFile > ${crIN}/.temp
		if [[ $verbose ]]; then
		echo $cmd
		fi
		eval $cmd
		#returns an R file with the TSO replaced with the 13 bp 10x Genomics sequence
		mv ${crIN}/.temp $convFile
		echo " ${convFile} adjusted"
		done
		fi

sub/FilterSmartSeqReadUMI.pl

+189 −189

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