remove TSO from ICELL8 and update docs for chemistry (3941fb43) · Commits · github_fork / Universc

README.Rmd

+2 −0

Original line number	Diff line number	Diff line
		@@ -1076,6 +1076,8 @@ Mandatory arguments to long options are mandatory for short options too.
		-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
		5′ scRNA-Seq ('SC5P-PE') is available only for 10x Genomics, ICELL8, SmartSeq, and STRT-Seq technologies
		All other technologies default to 3′ scRNA-Seq parameters. Only 10x Genomics and ICELL8 allow choosing which to use.
		-n, --force-cells NUM Force pipeline to use this number of cells, bypassing the cell detection algorithm.
		-j, --jobmode MODE Job manager to use. Valid options: local (default), sge, lsf, or a .template file
		--localcores NUM Set max cores the pipeline may request at one time.

README.html

+2 −0

Original line number	Diff line number	Diff line
		@@ -539,6 +539,8 @@ Mandatory arguments to long options are mandatory for short options too.
		-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
		5′ scRNA-Seq ('SC5P-PE') is available only for 10x Genomics, ICELL8, SmartSeq, and STRT-Seq technologies
		All other technologies default to 3′ scRNA-Seq parameters. Only 10x Genomics and ICELL8 allow choosing which to use.
		-n, --force-cells NUM Force pipeline to use this number of cells, bypassing the cell detection algorithm.
		-j, --jobmode MODE Job manager to use. Valid options: local (default), sge, lsf, or a .template file
		--localcores NUM Set max cores the pipeline may request at one time.

README.md

+2 −0

Original line number	Diff line number	Diff line
		@@ -1076,6 +1076,8 @@ Mandatory arguments to long options are mandatory for short options too.
		-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
		5′ scRNA-Seq ('SC5P-PE') is available only for 10x Genomics, ICELL8, SmartSeq, and STRT-Seq technologies
		All other technologies default to 3′ scRNA-Seq parameters. Only 10x Genomics and ICELL8 allow choosing which to use.
		-n, --force-cells NUM Force pipeline to use this number of cells, bypassing the cell detection algorithm.
		-j, --jobmode MODE Job manager to use. Valid options: local (default), sge, lsf, or a .template file
		--localcores NUM Set max cores the pipeline may request at one time.

launch_universc.sh

+71 −2

Original line number	Diff line number	Diff line
		@@ -232,7 +232,10 @@ Mandatory arguments to long options are mandatory for short options too.

		-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'
		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: 'SC3Pv2' (default), 'SC5P-PE', 'SC5P-R1', or 'SC5P-R2'
		5′ scRNA-Seq ('SC5P-PE') is available only for 10x Genomics, ICELL8, SmartSeq, and STRT-Seq technologies
		All other technologies default to 3′ scRNA-Seq parameters. Only 10x Genomics and ICELL8 allow choosing which to use.

		-n, --force-cells NUM Force pipeline to use this number of cells, bypassing the cell detection algorithm.
		-j, --jobmode MODE Job manager to use. Valid options: 'local' (default), 'sge', 'lsf', or a .template file
		--localcores NUM Set max cores the pipeline may request at one time.
		@@ -2637,12 +2640,78 @@ else
		fi

		if [[ $chemistry == "SC5P"* ]] \|\| [[ $chemistry == "five"* ]]; then
		#remove TSO adapters (from ends)
		sed -E '
		/^TTACTATGCCGCTGGTGGCTCTAGATGTGAGAAAGGG/ {
		s/^TTACTATGCCGCTGGTGGCTCTAGATGTGAGAAAGGG/GGG/g
		n
		n
		s/^(.{34})(.{3})/\2//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		sed -E '
		/^AGATCGGAAGAGCGTCGTGTAGGG/ {
		s/^AGATCGGAAGAGCGTCGTGTAGGG/GGG/g
		n
		n
		s/^(.{21})(.{3})/\2//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		sed -E '
		/^GCGTCGTGTAGGG/ {
		s/^GCGTCGTGTAGGG/GGG/g
		n
		n
		s/^(.{10})(.{3})/\2//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		sed -E '
		/^TGTGAGAAAGGG/ {
		s/^TGTGAGAAAGGG/GGG/g
		n
		n
		s/(.{9})(.{3})/\2//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#remove TSO adapters (from after cell barcode) #<- confirm tag sequence with Takara reps (appears to be CB-UMI-GGG)
		sed -E '
		/^(.{11})(.{14})TTACTATGCCGCTGGTGGCTCTAGATGTGAGAAAGGG/ {
		s/^(.{11})(.{14})TTACTATGCCGCTGGTGGCTCTAGATGTGAGAAAGGG/\1\2GGG/g
		n
		n
		s/^(.{11})(.{14})(.{34})(.{3})/\1\2\4//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		sed -E '
		/^(.{11})(.{14})AGATCGGAAGAGCGTCGTGTAGGG/ {
		s/^(.{11})(.{14})AGATCGGAAGAGCGTCGTGTAGGG/\1\2GGG/g
		n
		n
		s/^(.{11})(.{14})(.{21})(.{3})/\1\2\4//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		sed -E '
		/^(.{11})(.{14})GCGTCGTGTAGGG/ {
		s/^(.{11})(.{14})GCGTCGTGTAGGG/\1\2GGG/g
		n
		n
		s/^(.{11})(.{14})(.{10})(.{3})/\1\2\4//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		sed -E '
		/^(.{11})(.{14})TGTGAGAAAGGG/ {
		s/^(.{11})(.{14})TGTGAGAAAGGG/\1\2GGG/g
		n
		n
		s/(.{11})(.{14})(.{9})(.{3})/\1\2\4//g
		}' $convFile > ${crIN}/.temp
		mv ${crIN}/.temp $convFile
		#convert TSO to expected length for 10x 5' (TSS in R1 from base 39)
		echo " handling $convFile ..."
		tsoS="TTTCTTATATGGG" #<- confirm tag sequence with Takara reps
		tsoQ="IIIIIIIIIIIII"
		#Add 10x TSO characters to the end of the sequence
		cmd=$(echo 'sed -E "2~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$tsoS'/" '$convFile' > '${crIN}'/.temp')
		cmd=$(echo 'sed -E "2~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$tsoS'/" '$convFile' > '${crIN}'/.temp') #<- confirm tag sequence (GGG) with Takara reps
		if [[ $verbose ]]; then
		echo technology $technology
		echo barcode: $barcodelength

man/launch_universc.sh

+4 −1

Original line number	Diff line number	Diff line
		@@ -257,13 +257,16 @@ Provides a conversion script to run multiple technologies and custom libraries w
		-c, --chemistry CHEM
		Assay configuration, autodetection is not possible for converted files:

		SC3Pv2 (default), SC3Pv3, SC5P-PE, or SC5P-R2
		SC3Pv2 (default), SC3Pv3, SC5P-PE, SC5P-R1, or SC5P-R2

		Chemistry can only be automatically detected for 10x Genomics Chromium as it relies
		on matches to a barcode whitelist. For other technologies we do not recommend changing
		the chemistry input. All samples are converted to contain the barcode and UMI in Read1
		as used for SC3Pv2. SC3Pv3 is only used for technologies with longer UMI.

		5′ scRNA-Seq ('SC5P-PE') is available only for 10x Genomics, ICELL8, SmartSeq, and STRT-Seq technologies
		All other technologies default to 3′ scRNA-Seq parameters. Only 10x Genomics and ICELL8 allow choosing which to use.

		-n, --force-cells NUM
		Force pipeline to use this number of cells, bypassing the cell detection algorithm.

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