support Sci-Seq-3 with dedicated subroutine for dual indexes (e8a2e8d8) · Commits · github_fork / Universc

README.Rmd

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Original line number	Original line	Diff line number	Diff line
	@@ -166,7 +166,7 @@ We are developing technologies to support dual indexes and full length scRNA kit

	Experimental technologies (not yet supported):		Experimental technologies (not yet supported):
	- inDrops version 3 (16bp 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, 22bp barcode): sciseq
	- SPLiT-Seq (10bp UMI, 18bp barcode): splitseq		- SPLiT-Seq (10bp UMI, 18bp barcode): splitseq
	- SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad		- SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad

	@@ -988,7 +988,7 @@ Mandatory arguments to long options are mandatory for short options too.

	Experimental technologies (not yet supported):		Experimental technologies (not yet supported):
	inDrops version 3 (16bp 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, 22bp 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)

launch_universc.sh

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Original line number	Original line	Diff line number	Diff line
	@@ -217,7 +217,7 @@ Mandatory arguments to long options are mandatory for short options too.

	Experimental technologies (not yet supported):		Experimental technologies (not yet supported):
	inDrops version 3 (16bp 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, 22bp 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)

	@@ -725,9 +725,9 @@ elif [[ "$technology" == "quartz-seq2-1536" ]]; then
	umilength=8		umilength=8
	minlength=15		minlength=15
	elif [[ "$technology" == "sciseq" ]]; then		elif [[ "$technology" == "sciseq" ]]; then
	barcodelength=10		barcodelength=22
	umilength=8		umilength=8
	minlength=10		minlength=22
	elif [[ "$technology" == "scrbseq" ]]; then		elif [[ "$technology" == "scrbseq" ]]; then
	barcodelength=6		barcodelength=6
	umilength=10		umilength=10
	@@ -2254,6 +2254,21 @@ else
	echo " ...barcode and UMI swapped for ${technology}"		echo " ...barcode and UMI swapped for ${technology}"
	sed -E '2~2s/(.{8})(.{10})/\2\1/' $convFile > ${crIN}/.temp		sed -E '2~2s/(.{8})(.{10})/\2\1/' $convFile > ${crIN}/.temp
	mv ${crIN}/.temp $convFile		mv ${crIN}/.temp $convFile

			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/' )

			echo " ...concatencate barcodes to R1 from I1 and I2 index files"
			# 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=${convI1} --additive=${convI2} --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		done
	fi		fi

man/launch_universc.sh

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Original line number	Original line	Diff line number	Diff line
	@@ -207,7 +207,7 @@ Provides a conversion script to run multiple technologies and custom libraries w

	Experimental technologies (not yet supported):		Experimental technologies (not yet supported):
	inDrops version 3 (16bp 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, 22bp 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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