add experimental technologies to docs (754f3e9f) · Commits · github_fork / Universc

README.Rmd

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		@@ -1015,6 +1015,14 @@ Mandatory arguments to long options are mandatory for short options too.
		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
		Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
		BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
		STRT-Seq (6 bp barcode, no UMI)
		STRT-Seq-C1 (8 bp barode, 5 bp UMI)
		STRT-Seq-2i (13 bp barcode, 6 bp UMI)
		SmartSeq2 (16 bp barcode, no UMI)

		-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

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		@@ -490,6 +490,14 @@ Mandatory arguments to long options are mandatory for short options too.
		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
		Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
		BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
		STRT-Seq (6 bp barcode, no UMI)
		STRT-Seq-C1 (8 bp barode, 5 bp UMI)
		STRT-Seq-2i (13 bp barcode, 6 bp UMI)
		SmartSeq2 (16 bp barcode, no UMI)

		-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

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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: "Wednesday 21 April 2021"
		date: "Thursday 22 April 2021"
		output:
		prettydoc::html_pretty:
		theme: cayman
		@@ -1015,6 +1015,14 @@ Mandatory arguments to long options are mandatory for short options too.
		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
		Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
		BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
		STRT-Seq (6 bp barcode, no UMI)
		STRT-Seq-C1 (8 bp barode, 5 bp UMI)
		STRT-Seq-2i (13 bp barcode, 6 bp UMI)
		SmartSeq2 (16 bp barcode, no UMI)

		-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

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		@@ -220,6 +220,14 @@ Mandatory arguments to long options are mandatory for short options too.
		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
		Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
		BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
		STRT-Seq (6 bp barcode, no UMI)
		STRT-Seq-C1 (8 bp barode, 5 bp UMI)
		STRT-Seq-2i (13 bp barcode, 6 bp UMI)
		SmartSeq2 (16 bp barcode, no UMI)

		-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'

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		@@ -210,6 +210,14 @@ 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
		Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
		BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
		STRT-Seq (6 bp barcode, no UMI)
		STRT-Seq-C1 (8 bp barode, 5 bp UMI)
		STRT-Seq-2i (13 bp barcode, 6 bp UMI)
		SmartSeq2 (16 bp barcode, no UMI)

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

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