update documentation for SCI-Seq (98062a04) · Commits · github_fork / Universc

README.Rmd

+6 −6

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		@@ -998,22 +998,22 @@ Mandatory arguments to long options are mandatory for short options too.
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2
		Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3
		SeqWell (12bp barcode, 8bp UMI): seqwell
		SPLiT-Seq (10bp UMI, 18bp barcode): splitseq
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 30bp barcode): sciseq

		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

README.html

+6 −6

Original line number	Diff line number	Diff line
		@@ -473,22 +473,22 @@ Mandatory arguments to long options are mandatory for short options too.
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2
		Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3
		SeqWell (12bp barcode, 8bp UMI): seqwell
		SPLiT-Seq (10bp UMI, 18bp barcode): splitseq
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 30bp barcode): sciseq

		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

README.md

+7 −7

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		@@ -6,7 +6,7 @@ affiliations:
		index: 1
		- name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"
		index: 2
		date: "Friday 16 April 2021"
		date: "Wednesday 21 April 2021"
		output:
		prettydoc::html_pretty:
		theme: cayman
		@@ -998,22 +998,22 @@ Mandatory arguments to long options are mandatory for short options too.
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2
		Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3
		SeqWell (12bp barcode, 8bp UMI): seqwell
		SPLiT-Seq (10bp UMI, 18bp barcode): splitseq
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 30bp barcode): sciseq

		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

man/launch_universc.sh

+4 −5

Original line number	Diff line number	Diff line
		@@ -193,10 +193,13 @@ Provides a conversion script to run multiple technologies and custom libraries w
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2
		@@ -206,13 +209,9 @@ Provides a conversion script to run multiple technologies and custom libraries w
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 30bp barcode): sciseq

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

		10x Genomics, ICELL8, inDrops-v2, and QuartzSeq2
		10x Genomics, ICELL8, inDrops-v2, inDrops-v3, SCI-Seq (2-level), SCI-Seq3, SmartSeq3, and QuartzSeq2

		Where no known barcodes are available all possible barcodes of the expected length are
		generated and converted if the permutations have not been computed already.

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