Merge branch 'dev' of github.com:minoda-lab/universc into dev (19e12489) · Commits · github_fork / Universc

launch_universc.sh

+29 −12

Original line number	Original line	Diff line number	Diff line
	@@ -20,7 +20,7 @@
	install=false		install=false

	######UniverSC version#####		######UniverSC version#####
	universcversion="1.1.4"		universcversion="1.1.6"
	##########		##########


	@@ -207,9 +207,9 @@ Mandatory arguments to long options are mandatory for short options too.
	C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq		C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq
	CEL-Seq (8 bp barcode, 4 bp UMI): celseq		CEL-Seq (8 bp barcode, 4 bp UMI): celseq
	CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2		CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
	Drop-Seq (12 bp barcode, 8 bp UMI): dropseq		Drop-Seq (12 bp barcode, 8 bp UMI): dropseq, nadia
	ICELL8 3′ scRNA version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2		ICELL8 3′ scRNA version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
	ICELL8 3′ scRNA version 3 (11 bp barcode, 14 bp UMI): icell8 or custom		ICELL8 3′ scRNA version 3 (11 bp barcode, 14 bp UMI): icell8
	ICELL8 5′ scRNA with TCR OR kit (10bp barcode, NO bp UMI): icell8-5-prime		ICELL8 5′ scRNA with TCR OR kit (10bp barcode, NO bp UMI): icell8-5-prime
	ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length		ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length
	inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1		inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
	@@ -225,7 +225,7 @@ Mandatory arguments to long options are mandatory for short options too.
	RamDA-Seq (16 bp barcode, no UMI): ramda-seq		RamDA-Seq (16 bp barcode, no UMI): ramda-seq
	SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
	SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
	SCIFI-Seq (27 bp barcode, 8 bp UMI		SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq
	SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq		SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq
	SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3		SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
	Smart-seq (16 bp barcode, No UMI): smartseq		Smart-seq (16 bp barcode, No UMI): smartseq
	@@ -257,8 +257,7 @@ Mandatory arguments to long options are mandatory for short options too.
	-p, --per-cell-data Generates a file with basic run statistics along with per-cell data		-p, --per-cell-data Generates a file with basic run statistics along with per-cell data

	--non-umi or --read-only Force counting reads by adding or replacing UMI with a mock sequence.		--non-umi or --read-only Force counting reads by adding or replacing UMI with a mock sequence.
	Available for: ICELL8, Smart-Seq2		Default for: Quartz-Seq, RamDA-Seq, Smart-Seq, Smart-Seq2, STRT-Seq, ICELL8 3-prime version2
	Default for: Quartz-Seq, RamDA-Seq, Smart-Seq, Smart-Seq2, STRT-Seq

	--setup Set up whitelists for compatibility with new technology and exit		--setup Set up whitelists for compatibility with new technology and exit
	--as-is Skips the FASTQ file conversion if the file already exists		--as-is Skips the FASTQ file conversion if the file already exists
	@@ -1172,8 +1171,9 @@ if [[ $verbose ]]; then
	fi		fi
	for key in ${keys[@]}; do		for key in ${keys[@]}; do
	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	readkey=$key		echo "key: $key"
	fi		fi
			readkey=$key
	list=()		list=()
	if [[ $readkey == "R1" ]]; then		if [[ $readkey == "R1" ]]; then
	list=("${read1[@]}")		list=("${read1[@]}")
	@@ -2037,12 +2037,25 @@ if [[ "$technology" != "10x" ]]; then
	#use SC3Pv2 (umi length 10)		#use SC3Pv2 (umi length 10)
	echo "Using 10x version 2 chemistry to support UMIs"		echo "Using 10x version 2 chemistry to support UMIs"
	chemistry="SC3Pv2"		chemistry="SC3Pv2"
			umi_default=10
	fi		fi
	if [[ "$chemistry" != "threeprime" ]] && [[ "$chemistry" != "fiveprime" ]] && [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then		if [[ "$chemistry" != "threeprime" ]] && [[ "$chemistry" != "fiveprime" ]] && [[ "$chemistry" != "SC3Pv1" ]] && [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC3Pv3" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then
	echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE, SC5P-R1, or SC5P-R2"		echo "Error: option --chemistry must be SC3Pv3, SC3Pv2, SC5P-PE, SC5P-R1, or SC5P-R2"
	exit 1		exit 1
	fi		fi
	fi		fi
			if [[ "$technology" == "10x" ]]; then
			#use SC3Pv3 (umi length 12)
			if [[ "$chemistry" != "auto" ]];then
			#use automatic chemistry detection
			echo "Detecting 10x chemistry automatically"
			chemistry="auto"
			#do not convert UMI
			umi_default=12
			umilength=${umi_default}
			umiadjust=0
			fi
			fi
	if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "icell8-5-prime" ]]; then		if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[ "$technology" == "icell8-5-prime" ]]; then
	if [[ $verbose ]]; then		if [[ $verbose ]]; then
	echo " Using $chemistry for $technology"		echo " Using $chemistry for $technology"
	@@ -2055,7 +2068,6 @@ if [[ "$technology" == "smartseq" ]] \|\| [[ "$technology" == "smartseq3" ]] \|\| [[
	exit 1		exit 1
	fi		fi
	fi		fi
	chemistry="SC3Pv2" #####KAI REMEMBER TO REMOVE THIS#####
	##########		##########


	@@ -2460,13 +2472,18 @@ if [[ $lock -eq 0 ]]; then
	fi		fi
	#for version 3		#for version 3
	cat ${v2} > ${v3}		cat ${v2} > ${v3}
			fi
			if [[ -f ${v3} ]]; then
			gzip -f ${v3}
			fi
			if [[ -f translation/${v3} ]]; then
			gzip -f translation/${v3}
	fi		fi
	if [[ -f translation/${v3}.gz ]]; then		if [[ -f translation/${v3}.gz ]]; then
	rm translation/${v3}.gz		rm translation/${v3}.gz
	awk -F , -v OFS="\t" '{print $1, "\t", $1}' $v3 > translation/${v3}		zcat ${v3}.gz \| awk -F , -v OFS="\t" '{print $1, "\t\t\t", $1}' > translation/${v3}
	gzip -f translation/${v3}		gzip -f translation/${v3}
	fi		fi
	gzip -f ${v3}
	echo " whitelist converted"		echo " whitelist converted"

	echo "verbose $verbose"		echo "verbose $verbose"
	@@ -3498,7 +3515,7 @@ if [[ $verbose ]]; then
	echo $chemistry		echo $chemistry
	fi		fi

	if [[ $chemistry == "SC5P"* ]] \|\| [[ $chemistry == "five"* ]]; then		if [[ $chemistry == "SC5P"* ]] \|\| [[ $chemistry == "five"* ]] \|\| [[ $chemistry == "auto" ]]; then
	r=""		r=""
	else		else
	r="--r1-length=$totallength"		r="--r1-length=$totallength"

sub/MakeNewReference.pl

0 → 100644

+66 −0

Original line number	Original line	Diff line number	Diff line
			#!/usr/bin/perl

			#########################################
			# #
			# Written by Kai Battenberg #
			# Plant Symbiosis Research Team #
			# #
			#########################################

			use strict;
			use warnings;
			use Getopt::Long;

			#####SCRIPT DESCRIPTION#####
			#Script "MakeNewReference.pl" given a genome file (FASTA), annotation file (GTF), and a genome name, generates a reference for cellranger.
			###########



			#####Options#####
			print "\n\#\#\#\#\#Running MakeNewReference\#\#\#\#\#\n";
			print "checking options.\n";


			#setting the default values.
			my $genome = "";
			my $annotation = "";
			my $name = "";

			#making the options into external arguments.
			GetOptions (
			'genome=s' => \$genome,
			'annotation=s' => \$annotation,
			'name=s' => \$name
			);

			#checking for sequence type
			if (!$genome) {
			die "USAGE: option --genome <FASTA file> is required.\n";
			}
			elsif (!$annotation){
			die "USAGE: option --annotation <GTF file> is required.\n";
			}
			elsif (!$name) {
			die "USAGE: option --name <reference name> is required.\n";
			}

			print "check complete.\n\n";
			##########



			#####MAIN#####
			print "making cellranger reference.\n";

			system "cellranger mkref --genome=$name --fasta=$genome --genes=$annotation";

			print "reference made.\n";
			print "\#\#\#\#\#MakeNewReference COMPLETE\#\#\#\#\#\n\n";
			##########



			#####SUB#####
			##########
			__END__

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