support inDrops-v3 with dedicated subroutine (186d5c7d) · Commits · github_fork / Universc

README.Rmd

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README.html

+3 −3

README.md

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launch_universc.sh

+38 −9

Original line number	Original line	Diff line number	Diff line
	@@ -216,7 +216,7 @@ Mandatory arguments to long options are mandatory for short options too.
	e.g. Custom (16bp barcode, 10bp UMI): custom_16_10		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

	Experimental technologies (not yet supported):		Experimental technologies (not yet supported):
	inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
	Sci-Seq (8bp UMI, 10bp barcode): sciseq		Sci-Seq (8bp UMI, 10bp barcode): sciseq

	-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)
	@@ -705,9 +705,9 @@ elif [[ "$technology" == "indrop-v1" ]] \|\| [[ "$technology" == "indrop-v2" ]]; t
	umilength=6		umilength=6
	minlength=16		minlength=16
	elif [[ "$technology" == "indrop-v3" ]]; then		elif [[ "$technology" == "indrop-v3" ]]; then
	barcodelength=11		barcodelength=16
	umilength=6		umilength=6
	minlength=8		minlength=16
	elif [[ "$technology" == "marsseq-v1" ]]; then		elif [[ "$technology" == "marsseq-v1" ]]; then
	barcodelength=6		barcodelength=6
	umilength=10		umilength=10
	@@ -1523,11 +1523,10 @@ else
	fi		fi
	if [[ "$technology" == "indrop-v"* ]]; then		if [[ "$technology" == "indrop-v"* ]]; then
	if [[ "$technology" == "indrop-v1" ]] \|\| [[ $technology"" == "indrop-v2" ]]; then		if [[ "$technology" == "indrop-v1" ]] \|\| [[ $technology"" == "indrop-v2" ]]; then
	${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir}		perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir}
	elif [[ "$technology" == "indrop-v3" ]]; then		elif [[ "$technology" == "indrop-v3" ]]; then
	#ignore barcodes in index (R1 only)		#allow for barcodes in index (I1) and R1
	cp ${whitelistdir}/inDrop_gel_barcode2_list.txt ${whitelistdir}/inDrop-v3_barcodes.txt		${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir}
	#${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir}
	fi		fi
	else		else
	#generating permutations of ATCG of barcode length (non-standard evaluation required to run in script)		#generating permutations of ATCG of barcode length (non-standard evaluation required to run in script)
	@@ -2175,6 +2174,36 @@ else
	sed -E '2~2s/^(.{8})(.{8}).{4}(.{6})/\1\2\3/g' > ${crIN}/.temp		sed -E '2~2s/^(.{8})(.{8}).{4}(.{6})/\1\2\3/g' > ${crIN}/.temp
	mv ${crIN}/.temp $convFile		mv ${crIN}/.temp $convFile
	done		done
			# inDrops: migrate dual indexes to barcode
			# https://github.com/BUStools/bustools/issues/4
			if [[ "$technology" == "indrop-v3" ]]; then
			echo " ...processsing for ${technology}"
			if [[ $verbose ]]; then
			echo "Note: inDrops v2 should be demultiplex by sample index I2 (R3 or 4) if multiple samples are sequenced"
			fi
			for convFile in "${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/' )

			# (R1 -> R2; R2 -> I1; R3 -> I2; R4 -> R1)
			# v3 : summer 2016 redesign requiring manual demultiplexing.
			# R1 is the biological read (R2).
			# R2 (i7) carries the first half of the gel barcode (I1). <- which cell
			# R3 (i5) carries the library index (I2). <- which sample/organism
			# R4 the second half of the gel barcode, the UMI and a fraction of the polyA tail (R1).
			# returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2

			echo " ...concatencate barcodes to R1 from I1 index file"
			# concatenate barcocdes from dual indexes to R1 as (bases 1-8 of the) barcode (bases 1-16), moving UMI to (17-22)
			# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters
			perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --ref_fastq=${convR1} --out_dir $crIN

			#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
			mv $crIN/Concatenated_File.fastq ${convR1}
			done
	fi		fi

	#QuartzSeq: remove adapter		#QuartzSeq: remove adapter
	@@ -2305,7 +2334,7 @@ else
	mv $crIN/SmartSeq3_parsed_I2.fastq ${convI2}		mv $crIN/SmartSeq3_parsed_I2.fastq ${convI2}

	echo " ...concatencate barcodes to R1 from I1 and I2 index files"		echo " ...concatencate barcodes to R1 from I1 and I2 index files"
	# filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters		# concatenate barcocdes from dual indexes to R1 as barcode (bases 1-16)
	perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN		perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN

	#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)

man/launch_universc.sh

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -206,7 +206,7 @@ Provides a conversion script to run multiple technologies and custom libraries w
	e.g. Custom (16bp barcode, 10bp UMI): custom_16_10		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

	Experimental technologies (not yet supported):		Experimental technologies (not yet supported):
	inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
	Sci-Seq (8bp UMI, 10bp barcode): sciseq		Sci-Seq (8bp UMI, 10bp barcode): sciseq

	A barcode whitelist is provided for all beads or wells for the following technologies:		A barcode whitelist is provided for all beads or wells for the following technologies:

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